This would be a good time to check T. I. R. on your cylinder block and cylinder head mating surfaces... grind if neccessary. A little hard to fix when its in the truck.
I tend to be overly anal about it if I get the chance to check things from the comfort of anywhere other than with my feet wedged between the block and a frame rail, so personally I'd check as many of the bearing and mating surfaces as you can, depending on how much you wanna take apart. Machine as neccessary, if youre going through the work to do the swap, you want that thing to run (and last) like a brand new motor.
At this point I'd also have to ask if youre just looking for a CTD Ramcharger, or if you're lookin for a 500hp CTD Ramcharger. Depending on you're answer to that, I think I'd suggest a totally different set of things to check/fix.