First off...what is a Cummings? Never heard of them....millions of CUMMINS though!
Being as you have a mechanical injection engine (no ECM's to deal with) it should be fairly simple mechanics wise(no electrical connections or computers to program), pretty much remove old components and bolt in "new", parts wise it could be a little more involved.
You would first need to find a transmission with the right bellhousing pattern(SAE #1 in your case, probably one the most common) to bolt to your Big Cam, as well as determine how the engine/transmission is mounted to the frame (some use the bellhousing as rear engine mounts, some use transmission mounts. When you find the transmission, buy the trans and all linkages/shifter/mounts/etc. You would also need the right torque converter for a 350 Big Cam (the military one probably would have used a Detroit Diesel 8V92(2 stroke, high revving engine) which has a very different torque curve to your inline 6).
Most 9speeds were direct drive back then, but there is a chance it is OD. A used 9speed probably is worth very little, but anything helps.
Here is a link to a parts supplier to give you an idea on ht750 pricing.
A $4000 plus 9speed sale budget is going to be tight unless you can snag a good deal or do the labor yourself.
Your best bet is to find a smaller, local HDT repair shop and talk to them about a swap.