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[WeeHooker]

Yea, you can cut Thule bars to any size you like. Mine are 52".
FWIW,I hauled yaks, canoes and aluminum boats regularly on my factory racks w "yakathule" bars last year. Many were big/heavy boats ( i.e 17'4"-120#). Hauling them upside down helps the find force push them down/into the racks vs lifting them. Also , I do use bow lines but only on boats longer than 14' and/or of flexible materials. ( I've hauled 14' aluminum boats on my Tacoma's roof racks for thousands of mile with no bow line at all.) I do use good rachet straps at the mid section of the boat though. Never had a problem.
Having said that, I'll pass on a few tips I've learned over the years of "car topping" boats that make it easier.

First, make yourself a set of nylon tie in loops to attach to your truck as follows:
Get a couple of 16+/-" 1"wide nylon strapping pieces (like off the ends of those rachet straps) and double them over into a loop. Then, punch a matching hole in the ends ( a hot nail works good here) big enough to put a 1/4" bolt through. Now, go under your hood and find one of your forwardmost fender attaching bolts ( or a hole in the fender flange) on both sides of the engine compartment. Pull a fender bolt and reinstall it going through the doubled nylon first. (or install a new bolt and nut in a vacant hole to accomplish the) same. What you will end up with is a nylon loop that is now fixed to the fender. This loop can now be flipped in or out of the hood as needed, to provide a secure tie in point that keeps ropes off your hood, fender , etc. This ten cent fix works GREAT and disapears when you don't need it.
If you want to go a step further, make a V or Y shaped bow line for your favorite boats and end them with (3) Carabinas. This allows you to quickly clip into those truck loops and the boat. It has the added benifit of putting your boat in the sme exact location on the racks every time AND iliminates chances for bad knots. hth