The TH400 with AMC bellhousing had a unique tailshaft that only worked with the Borg Warner quadratrac transfer case. You will need a different tailshaft and an adaptor, along with a transmission rebuild to install it, in order to bolt it to the New Process bolt pattern. You will likely have driveshaft issues because of the length. You will also need a different flexplate. Pretend its a Quadratac 1979 CJ7 with 258 for the flexplate.
One cool thing about the TH400 is the kickdown. Its an electronic switch. On some FSJs there was a switch similar to the one that controls your brakelights except on the gas pedal, to let it know when to downshift. On my CJ7 its a cable jobber off the throttle plate to the switch. That makes the installation more flexible.
The TH400 is exactly as strong and reliable as a TF727. A TF727 is much better than your old 998 and it uses all the old linkages, and it can be purchased for less than the cost of the fancy TH400 tailshaft adaptor. Generally installing a TH400 is a waste of time and money, but that's your decision to make.