Thats the other thing I disconnected was my vacuum lines. For some reason my car has "California EGR 85" Vacuum configuration in the engine compartment and its a real spider web compared to the simpler vacuum configuration of other models. It has a Vacuum Amplifier on the fender for the Feed to the transmission instead of a direct feed from the modulator and it also has an EGR. When i pulled my Injection Pump I had to drop my oil filter tower and to get to those 27 mm oil hose nuts, I simply disconnected all the vacuum lines to avoid anything getting broken. I followed the diagram carefully when I put it back together...but I know somewhere something is leaking.
However its my understanding theat the Vaccum modulator only causes smoother shifting, not missed shifting. Rebyuilding an Automatic Trans was always a "Next Year" project because personally I love 5 speed manual...