Many points covered are good suggestions however I strongly disagree over some transmission opinions in this thread.
IMHO (owning and operating a diesel tranny shop) the NV4500 is a last resort option for a swap, has terrible ratios and very poor quality parts support for the normal person's budget. Most NV4500 aftermarket parts are poor and cores are artificially expensive. New Venture doesn't exist anymore. There are no such thing as OE quality parts for them.
The NV5600 does not impress me, shift feel is the worst of any pickup tranny ever made and reliability is worse than the NV4500.
The ZF 5 speeds shift much better than a 4500 or 5600, but they will not handle stupidity as well as the 4500 will (crashing gears, rapid 1st-reverse shifts, etc). The ZF 5 speeds will handle any power a single disc clutch will as long as you don't treat it like a race car. ZF 5 speeds are cheap and very common. Far more diesel ZF's were made than NV4500's. The diesel ZF 5 speed ratios are perfect for a diesel- apples to oranges with NV4500 ratios.
The ZF 6 speed is a far better tranny than the 5600, it's shift feel makes it the only pickup six speed I would have in my own truck. it has a built in oil pump and runs on cheap fluid. These trannies will take a hell of a beating, their internals and bearings are atleast twice the size of NV4500 parts.