As I understand it (EFIGuy will know for sure) an A9L can be turned into an A9P with the Quarterhorse except for the difference in the neutral/drive switch wiring. What I experienced was when pushing in the clutch while rolling to a stop, the engine would instantly drop to idle speed. Sometimes a little below, then catch itself and stabilize. Except when it didn't. And it died. With the VSS, I observed that when I pushed the clutch in while approaching a stop, the idle would hang a little high- maybe 100 rpm or so- until I came to a complete stop. Then it would settle down.
I learned my way around Binary Editor when I ran EEC-IV, mostly using a Tweecer, but I didn't change much. It was primarily so I could enable EDIS, secondarily to take advantage of the cam I had. I switched to a Quarterhorse a few years ago, then made major changes to run the 408. EEC-V came about mainly because I pulled the NV4500 in favor of a 4R70W and I didn't want a standalone transmission controller. I was interested in the challenge of using the Explorer stuff (maybe I'm a masochist).
You should check for codes. Not all of them will turn the check engine light on.
As for reflashing, that's a gray zone.