When you disconnected the VR, did you plug both ends? If you left open the supply side where it splits from the BFS vacuum supply line, you were running without benefit of the modulator. I don't know what linkage you can adjust to compensate. In fact, I don't know what linkage at all you can adjust besides the shift linkage which aligns the shift lever with the shift gate, and the pressure control cable which adjusts shift points. Removing the VR shouldn't affect all the shifts all the time.

When the car performs to your expectations, there's little reason to touch it. When it doesn't and the indication is there's a fault in the pre-OBD EDS, there's simply no good documentation on diagnosing the problem. Someone with time and resources should smog check a 2.5 before and after the conversion to determine the environmental impact. Then delete the report because I believe it's more environmentally sound to keep a 2.5 on the road than replace it with another car... while the next owner of the 2.5 does the conversion to keep it on the road

Sixto
MB-less