My dad has a 87 f-350 6.9 dually 4x2 we use to pull one of our cargo trailers, with the c6 and 4.10s, and a banks kit. plenty of power for a 10k trailer. pulling we get around 14/15, mostly town driving. A c6 tranny is hard to kill. I like the 6.9 it is the same block as the 7.3 so it should be interchangeable. there is a aftermarket turbo for the 6.9, I have seen them, I found one on ebay for like 600. I decided against it as I have way to many projects.
Centurion is well know for upgrading fords (they made a 4 door bronco) everything I have ever seen them do has been really nice.
sorry I don't know about the 4x4 set ups in the f-350s of those years. I have a 89 gas full size 4x4 bronco with the twin I beam set up, with c6 tranny and never had a problem and I run 35s with an open front and a locker in the back.
hope this helps