Wanted to see if I could get some thoughts as to where I go next. Just had a "newer" Trans installed (140k miles) and TC rebuilt and it seems like I've developed a high initial idle. It's right about 1000 rpm's during start up idle. I'm pretty sure that's why I get a clunk after I put it in reverse even after mashing on the brake. I got a long spline installed to lessen that reverse clunk so I'm pretty sure it's due to the high initial idle. The high idle goes away after I drive it for a bit and settles down to 650-700 rpm.
I've read threads about cleaning the throttle body and checking for codes. For a "newer" trans, I still have a bit of weird shifting but I'm leaning towards the engine rpms all over the place. Damnit - should have gone with the H55F!
I never noticed it before but there seems to be a gap where the gasket is. Maybe a bad gasket letting air in causing high idle?
Worth checking (easy to check by spraying WD40 or starting fluid at that gap), but also get the FSM procedure to set up the kickdown cable correctly. A badly adjusted kickdown cable can cause odd shift points and general misbehavior. I would assume few/no transmission shops would set up the kickdown cable correctly.
Another source of vacuum leak that I've encountered is the little adjusting screw on the top of the throttle body (facing forward). The o-rings get crusty and do nothing. It's easy to pull the screw and replace the o-ring (remember to count the turns as you remove so you can return it to the same setting).
There are many things that can cause a high idle. Here's a diagnostic decision tree from the factory service manual. This doesn't match your symptoms exactly, but shows the number of systems on the 3FE that can affect idle speed.
