You MUST use a 5.9 computer if running a 5.9. The 5.2 will run the 5.9 albeit lean. Going from an automatic to a manual, you do not need to change the computer in trucks 95 and earlier. Need a new comp if vice versa (manual to auto). Comps must be from 94-95 models only

If budget is an issue, just buying the t-56 will blow it, let alone the clutch hydraulics. The NV4500 is the superior tranny is a towing truck- its behind the diesels albeit in a beefed version. You need the gas version- theres about a million little stupid parts for a swap like this so I hope there are some junkyards near you b/c getting it on ebay will be $$$$. Parts truck is always a good idea

400 hp will require a pretty stout cam. Roller cams ain't cheap. Hughes has some good ones though that may get you near it and keep respectable low end torque. 360 hp at the flywheel more realistic for a towing engine.

The RHS/engine quest heads from Hughes are a good way to avoid machine work costs and get the thicker decks. They flow slightly better than stock as well so that helps your power wish. Still not cheap

I've just spent alot of money
550 for 5.9 JY engine with mid level miles
1000 for nv4500 in good shape
200 for nv4500 bell
100 for hydraulics and pedals if you're lucky
350 for cam
1200 for heads
140 for 5.9 flywheel
150 for clutch kit
$$$ aside for driveshaft work possibly (shorter or longer?)
60 new crank sensor for manual tranny
60 special fluid for nv4500