Parts availability
I don't think you will want to pay the price for dealer parts even if they are still in stock, which I doubt, but everything you want can be had from a salvage truck. I have not done the 4500 route but have the parts to change an automatic to manual using the Getrag setup. I read in the posts here that many are going with the aftermarket rebuild on the automatic and are getting very good result. I have two automatics and two manuals. Except for having to shift, I prefer the manuals two to one over the automatics. If I had the money, I would try an aftermarket rebuild. It is at least possible that the later transmission with a lock up converter would give near equal service to the manual. Should you elect to go with an automatic, be careful who you chose to do the work. Not many are familiar with the needs of the Cummins powered application.
But to your original question, you can do the swap and you won't have to build anything from scratch. You will need different drive shafts. You will probably have to modify the crossmember for the rear of the 4500. You will have to do some junk yard digging.
What you are wanting to do has been done. Hopefully someone who has done it will offer better suggestions. An expression I have heard associated with the computer/electronics industry is 'plug and play'. This is not plug and play.
From the agravation I have experienced with my automatics, I suspect I know why you want to change out the slush box. TPS, heat buildup, OD repeatedly shifting in and out.
James