Any diesel used in ford pickups up until 2011 was an international/Navistar engine.
A dt466/360 wouldn't really "bolt up" per say. You'd likely need different motor mounts, radiator, exhaust, driveshaft, and some fab work to get it in there. A donor bus would have all that, but being away from home, a new swap complicates it quite a bit.
AT545's are pure mechanical. No solenoids or sensors to go bad so you can count that out for your trans problems. I don't think any at545's were ever 5 speed. So that craigslist poster is confused and that transmission should work for you.
The 2000 series on ebay is a far better trans then the at545, but it also requires a computer to run and a wiring harness. Neither of those seem to be included in that ebay listing.
Quickest route to get back on the road would be the 6.9 you found in the pickup and then that trans on craigslist. That is if all the pieces are in good working order like advertised
If you want to start swapping stuff and engineering a better bus, then you're looking at considerably more time, and from what I've gathered, you're not doing this yourself, so time=money.