Didn't the viper truck get a zero towing capacity rating when equipped with that trans because it can't handle the constant heavy load?
If I was on a budget I would just take the stock 5.9 mag completly apart, square the deck and mil it about .030 to get near zero deck (measure to be sure but this is what I typically find gets me within .005), then run a MrGasket thin head gasket to get nice tight quench and more compression, this make more power MPG and makes it very knock resistant. Do a basic 3 angle valve job, ignore the cracks they are there but don't seem to ever hurt anything. If your budget allows get the cam re-ground by deta cams if not then use the 318 cam, it is slightly better cam than the 5.9 comes with and the 5.9 cam is bigger than the 300HP crate motor cam so it ain't too bad when talking free cams. If you can afford the re-grind (around $100 with shipping) tell em you want as much lift as possible and no more than 205 duration at .050 single pattern and 110LSA. If you really want 400 hp you will need a better intake, the hughes airgap is good for that and readily available but you lose some valuable TQ down low in a heavy truck. There is no way around it as the very long runners in the stock intake make a lot of TQ down low but you have to shorten them up to get HP, the airgap keeps the air much colder going in the engine and that helps some but when towing there is still a significant loss of usefull TQ.
The 408 strokers work awesome for trucks but DO NOT GET THE EAGLE CAST CRANK! I have personally seen a few of them break in very mild aplications, get the SCAT crank and external balance it, internal is better but you might as well cough up for forged at that point because you will need expensive mallory metal to internally balance the cast one and it will cost as much as the forged one and not be as good. Also if you go stroker you will want to shlep on down to your favorite junk yard and pull a set of fuel injectors off a 460 ford engine. The 408 can be very rewarding but tends to sno-ball in cost.
If you have to bore your block but stil want to be a little cheaper than the stroker then a set of KB107s help reduce cost by eliminating block milling then you can use that money to balance it witch helps if you are turing up the RPM.
Another trick I found that helps and is free (if you do it yourself) is to reduce the PR pinch, even grinding out about .050 on the PR bump will improve the injectors shot at the back of the vave instead of just squirting fuel into the side of the port. No matter what you settle on for a plan this helps a magnum motor.
If you are on a really tight budget you coud buy the 5.9, put in the 5.2 cam, pull the heads and buy one MrGasketMLS head gasket, take it apart and use the thin outer layers for individual head gaskets, this will get you almost good quench and a little more compression. Make sure you block and heads are both very clean and smooth before doing this and I spray both sides of the gasket with copper coat if the block and heads are not freshly resurfaced. This motor will pull quite a bit harder than the old 5.2.