If he is putting the 01 6.5 into the 83, then later is planning on bumping up to descent turbo and bigger injection pump...
Yes now would be the time to correct interior issues of the 6.5 before install. Pop the heads, check for cracks, new seals etc. I would also do new bearings, and balance the lower assy. To address timing chain, water pump, balancer, etc. issues at that time makes sense if affordable. If the interior is all that can be afforded, then skip timing system forward until later, as balancing the internals is more crucial.
A huge mistake a lot of people make is to not determine the proper build and costs in the beginning. figure exactly what you want, figure cost of total project and decide if it is all worth it or only partial. Knowing the block and head condition is a very important thing to begin with. I have seen many people buy loads of parts to learn five minutes too late their block was crap.
When doing a swap, take your time and build it right the first time. Get it all done at once if at all possible, that way once it is together you can get the long life without all the repairs and issues.