Anyone with a 4.0 know how the transmission and back harness plugs in?

[cp2295]

Okay so doing the 3.0 to 4.0 swap and I just noticed that the 3.0 has the wiring harness all In one, the transmission and engine harness is all one setup, no separate plug ins. The 4.0 I bought came with the engine wiring harness but I see that there's plug ins on the back of the engine that look like they'd plug into transmission and back stuff. When I go to the junkyard what will I need? The engine harness I have now is for an automatic, but I have a manual tranny for the 4.0. Will it matter what harness I get or will the auto tranny stuff just not plug in? And what about the speed sensor and all that stuff?

I got a 99 3.0. A 98 4.0 and 98-2001 model m5od manual tranny going into the ranger in place of the 3.0.
Thanks for the help!

Sorry for all the posts btw haha, just got a lot of questions.