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Alright, I decided to take care of the Big 3 Upgrade on the truck this evening, but it was a bit of a "hunt and peck" since the examples, pictures and write-ups seem to be scattered or non-existent for second-gen Frontiers. This is also the reason I decided to throw up a crude write-up, just in case someone else was looking to take care of this...as well as some very basic...very simplistic testing. First thing's first...where we're starting:
The first thing I did (after some minor testing) was to take out the battery just to avoid any unintentional fried wires. While I had the battery out I also dismantled the battery clamps to prepare for my new ones.
I wanted to get the "hard to reach" crap out of the way first, so I jacked up the truck, pulled the front passenger tire so I could remove the inner wheel cover. This is held in with a handful of screws and plastic tabs.
This has been covered thousands of times...but just in case you need a refresher on the tabs...use a flat screwdriver under the inner portion, pop it out slightly, and then use the screwdriver to pull out the entire clip.
Once the inner cover is off you'll have a much easier time accessing the wire you need from the alternator. It's tucked under the bright red cover:
Just pop the cover off and you'll see the nut you need to remove to access the mounting bolt.
You'll need a little wiggle room to put everything together, so on the large bundle of wires, pry up the tab to release them from the plastic holder. As for the plug on the alternator, just press in the tab and pull...this should give you just enough room to work.
Remove the nut and existing wire. Take note of the tabs on the existing wire, these fit into corresponding slots on the alternator, so you'll need to make sure you reinstall this wire correctly.
When you put the new wire on the post, to ensure everything sits nice and flush and that you'll be able to use the rubber cover again, make sure you install the wire as shown:
With the wire in place, reinstall the original wire on top of it and tighten the nut. If you have some extensions and swivels...now would be a good time to get them out. This was by far the most pain-in-the-*** part of the entire procedure.
Once tightened, reinstall the rubber cover and route the wire out of the way...away from any areas with excessive heat or where rubbing may occur. I used the existing wire bundle to tie to. I was going to use a protective sleeve here...but didn't, for a few reasons...I was going to fuse it anyway, the route I took to mount it is fairly secure...and most importantly...I did not have any split loom big enough for the wire. Most likely my OCD will kick in and I will get some and cover the wire.
Once that was done, the rest of the work takes place from above, so I went ahead and put the wheel well cover and tire back on, pulled the truck off the jack stand, and turned my attention to under the hood (plus, lowering the truck made it easier to work in the engine compartment. Where you decide to upgrade/add the engine-to-chassis ground is up to you, but I decided to simply replace the dental floss the is tucked under the air filter...so, time to remove some parts:
The wire I'll be replacing is directly under the filter, highlighted here in green:
Rather than add to this wire, I completely replaced it, but only because I know for a fact that this is purely a simple ground wire. If you upgrade this exact wire, take care to told the bolt underneath or you'll twist this entire bracket when loosening the bolt.
Once the old wire is removed, I took a Dremel with a wire brush attachment and cleaned up the two contact points, getting rid of any paint or buildup so the wire would make good contact on the metal.
I shortened the ground wire that was supplied to the exact length I needed and bolted it in place. To avoid rust I used a bit of clear Rustoleum over the bolt where I exposed the bare metal.
Next was the battery-to-chassis ground. Again, I did not replace the existing wire...I added to it. There was already some grounding points tucked behind the battery, so I picked one and took the Dremel to it.
I took one of the ends I previously cut off and attached it to the existing positive wires to give a bit of an extension for the battery clamp.
I decided to mount the fuse to the front side of the fuse box. The power wire from the alternator routes into this and then to the new positive battery terminal clamp.
The new terminals were a simple bolt-in design. The negative side now has the original wire, my upgrade and the wire going to my Anderson plug. The positive is much the same...original harness, upgraded alternator wire and Anderson positive wire. I also have one more slot in the new plugs which I am reserving for the winch power and ground wires.
The old fuses/wires from the original positive plug are secured in place, although a little 'in the way' if I need to access the newly installed fuse.
...and everything cleaned up...
...now you just have to hop back in the truck and reprogram all of your radio stations! (And probably drive it to reset the Slip light)
...and of course the "after" picture. Can you see all the extra horsepower? There's at least like 400...maybe 450.
In all seriousness though, the biggest reason I did this was for future upgrades, sound system, winch, lights etc. With running all my future off-road lights, the possibility of upgrading the amp, subs etc...I want to be able to get the most out of my electrical system. This is not some kind of superfix for any particular issue, but it should help with some future upgrades I have planned.
So...did it work?
Before I did this upgrade, I ran a very basic test. I hooked up my multimeter and started the truck up. With the truck running and everything I could possibly turn off...turned off, I was showing an average of 14.2 volts. I then switched everything on...every light I have (headlights, KCs, LEDs etc), A/C, fans, backseat TV, cranked the music, heated seats...everything I could find. At that point, my multimeter was averaging about 13.2 volts.
After the install, I ran the exact same test. With everything shut off I was reading an average of 14.3 volts. After switching everything on...I showed 14.15 volts...with the lowest reading over a few minutes at 14.1 volts. Seems like everything is working correctly and ready for future upgrades!

DISCLAIMERS
- You are messing with your electrical system, if you mess up, get electrocuted, fry your system...it's on you, this is just a guide to what I did in hopes that it may help you find, locate and get you in the right direction.
- My steps may not exactly match what you need/want to do. I took this time to add new battery post clamps which is a step you may not take. I also fused the positive wire...which is up for debate as to whether it is "necessary" or not. I would rather be safe, and for various other reasons...I fused it.
- I'm a tinkerer...so my way may not be the right way or the professional way...but it works for my purposes.
- This is an upgrade, not a replacement. Remember that. Unless you are absolutely certain that you can replace a wire with another wire...don't. Leave the existing wiring in place and just add in the upgraded connection. For example, the negative battery terminal to the chassis ground has a sensor in place that the alternator needs for how many amps it should be putting out. DO NOT replace this cable.
The first thing I did (after some minor testing) was to take out the battery just to avoid any unintentional fried wires. While I had the battery out I also dismantled the battery clamps to prepare for my new ones.

I wanted to get the "hard to reach" crap out of the way first, so I jacked up the truck, pulled the front passenger tire so I could remove the inner wheel cover. This is held in with a handful of screws and plastic tabs.

This has been covered thousands of times...but just in case you need a refresher on the tabs...use a flat screwdriver under the inner portion, pop it out slightly, and then use the screwdriver to pull out the entire clip.

Once the inner cover is off you'll have a much easier time accessing the wire you need from the alternator. It's tucked under the bright red cover:

Just pop the cover off and you'll see the nut you need to remove to access the mounting bolt.

You'll need a little wiggle room to put everything together, so on the large bundle of wires, pry up the tab to release them from the plastic holder. As for the plug on the alternator, just press in the tab and pull...this should give you just enough room to work.

Remove the nut and existing wire. Take note of the tabs on the existing wire, these fit into corresponding slots on the alternator, so you'll need to make sure you reinstall this wire correctly.

When you put the new wire on the post, to ensure everything sits nice and flush and that you'll be able to use the rubber cover again, make sure you install the wire as shown:

With the wire in place, reinstall the original wire on top of it and tighten the nut. If you have some extensions and swivels...now would be a good time to get them out. This was by far the most pain-in-the-*** part of the entire procedure.

Once tightened, reinstall the rubber cover and route the wire out of the way...away from any areas with excessive heat or where rubbing may occur. I used the existing wire bundle to tie to. I was going to use a protective sleeve here...but didn't, for a few reasons...I was going to fuse it anyway, the route I took to mount it is fairly secure...and most importantly...I did not have any split loom big enough for the wire. Most likely my OCD will kick in and I will get some and cover the wire.

Once that was done, the rest of the work takes place from above, so I went ahead and put the wheel well cover and tire back on, pulled the truck off the jack stand, and turned my attention to under the hood (plus, lowering the truck made it easier to work in the engine compartment. Where you decide to upgrade/add the engine-to-chassis ground is up to you, but I decided to simply replace the dental floss the is tucked under the air filter...so, time to remove some parts:

The wire I'll be replacing is directly under the filter, highlighted here in green:

Rather than add to this wire, I completely replaced it, but only because I know for a fact that this is purely a simple ground wire. If you upgrade this exact wire, take care to told the bolt underneath or you'll twist this entire bracket when loosening the bolt.

Once the old wire is removed, I took a Dremel with a wire brush attachment and cleaned up the two contact points, getting rid of any paint or buildup so the wire would make good contact on the metal.

I shortened the ground wire that was supplied to the exact length I needed and bolted it in place. To avoid rust I used a bit of clear Rustoleum over the bolt where I exposed the bare metal.

Next was the battery-to-chassis ground. Again, I did not replace the existing wire...I added to it. There was already some grounding points tucked behind the battery, so I picked one and took the Dremel to it.

I took one of the ends I previously cut off and attached it to the existing positive wires to give a bit of an extension for the battery clamp.

I decided to mount the fuse to the front side of the fuse box. The power wire from the alternator routes into this and then to the new positive battery terminal clamp.

The new terminals were a simple bolt-in design. The negative side now has the original wire, my upgrade and the wire going to my Anderson plug. The positive is much the same...original harness, upgraded alternator wire and Anderson positive wire. I also have one more slot in the new plugs which I am reserving for the winch power and ground wires.

The old fuses/wires from the original positive plug are secured in place, although a little 'in the way' if I need to access the newly installed fuse.

...and everything cleaned up...

...now you just have to hop back in the truck and reprogram all of your radio stations! (And probably drive it to reset the Slip light)

...and of course the "after" picture. Can you see all the extra horsepower? There's at least like 400...maybe 450.

In all seriousness though, the biggest reason I did this was for future upgrades, sound system, winch, lights etc. With running all my future off-road lights, the possibility of upgrading the amp, subs etc...I want to be able to get the most out of my electrical system. This is not some kind of superfix for any particular issue, but it should help with some future upgrades I have planned.
So...did it work?
Before I did this upgrade, I ran a very basic test. I hooked up my multimeter and started the truck up. With the truck running and everything I could possibly turn off...turned off, I was showing an average of 14.2 volts. I then switched everything on...every light I have (headlights, KCs, LEDs etc), A/C, fans, backseat TV, cranked the music, heated seats...everything I could find. At that point, my multimeter was averaging about 13.2 volts.
After the install, I ran the exact same test. With everything shut off I was reading an average of 14.3 volts. After switching everything on...I showed 14.15 volts...with the lowest reading over a few minutes at 14.1 volts. Seems like everything is working correctly and ready for future upgrades!