On my '88/5.0 swap the adapter kit came with a filter relocation setup, new motor mounts, headers, and an extra volume oil pan.
The frame on the passenger side had to be slightly mod'd for the headers to fit but other than that, with an adapter kit, the engine slipped in.
Get one of the three wire engine harnesses or the harness that is on the donor vehicle.
Mine was out of a ’93 Stang, 5.0L, manual so I got the engine harness and computer,, that was all I needed.
the only problem I got into was the Fuel Pump wiring but a call to a Ford Rep straightened it out.
The engine harness on the 89, 2.9, should be a separate engine harness and easily removed.
The next thing is the trans, here there isn't much choices, just the C-4 auto or if you are auto you can put something together from your trans and the bell housing from the C-4. Check out the web for instructions.
Other auto trans may fit but the standard route is limited if not impossible to fit in and the linkage too, maybe a 5 sp with the internal hydraulic clutch.
I ran the 5.0 for five years before selling the truck, it ran the balls.
The motor mounts aren’t like the newer ones where you can just get them from Ford, you need adapter mounts made for the swap but there are a lot of them out there.
I used the complete swap kit for L&L Products and all went well but they are a little pricey or maybe you can get some off e-bay.
I used the OEM 2.9L/5 sp mount to mount up the C-4 bolted up so I went with it without a problem.
My C-4 had an Advanced Adapters T/C Adapter Plate to mount the stock 2.9L Transfer Case and again no problems.
I do not do a lot of heavy duty off roading so I think if you plan some HD stuff consider an HD T/C.
Luck to ya !
Ltr