im glad your concerned with your truck and having it run is well as possible but to be honest with you, in my opinion i wouldnt go changing a whole lot from factory spec.
exhaust- i have an 07 and from rockauto.com i can get a complete cat back exhaust (tail pipe, SS muffler, mid pipe, Y pipe) for a little less than 200 bux, thats if you need more than just a muffler. you can also find some very reasonably priced front and rear cats on that site too. as far as "high flow" goes i honestly dont know how much performance or efficiency you'll gain.
Fan clutch- i replaced mine like 40k ago, for like 60 bux orderd off that previously mentioned site, i gotta ask, why go electric? is there much benefit?
my 2 cents- truck health "DO FLUIDS" everything bumper to bumper, super easy to do the gear oil in the front and rear dif's, trasfer case lube change is done the same way also, pull the plug on your tranny pan and you'll get almost half your tranny fluid out, its not a full change/flush but if you do it every 20k or so it will make a difference (side note, these trucks call for nissan matic j/s/d and whatever else kinda fluid from the manufacture and its ridiculously over priced, i use valvoline MAXX LIFE in both my tranny and transfer case, its about a quarter of the price and says right on the back of the bottle its compatible with all nissan lubes) and obviously your engine oil.
you could also think about installing a catch can to keep the oily crap out of your intake, iv heard guys get 3-5 MPG difference after adding one of those. maybe a coolant flush? definitely new spark plugs as well. clean your mass air flow sensor.
i'm kindof drawing a blank now on what else you could do but im sure you get the jist, the truck was built healthy from the factory and all you gotta do to keep it that way is your basics, no super dooper after market needed.
just and fyi, my 07 has just under 180,xxx on it and ive been wrenchin on it since day one with zero major problems.
hope this helps! or at least gives you another perspective.