The 1998 4Runners never came with the Multi-mode transfer case, if that's what you mean by AWD, even if it's a Limited. The Multi-mode transfer case started on the Limited's in 1999.
Not any help bur I'm putting in a 5 speed in my 97 . Just installed the clutch pedal. Bout to drop tranny and be on the road. I have a repin chart no check engine code