Here is what happens - the EEC commands the tranny to shift - but since the tranny is a mechanical/hydraulic part, the shifts can't happen instantly. The EEC is programmed to command the shift anticipating the delay in the shift being completed. With a stock Mustang vs. a Mustang with gears, the time for the stock Mustang to do this is always slower than a Mustang with gears. That's because the Mustang with gears revs a lot faster. If you do additional mods to make more power, it will rev even faster and the problem will just get worse. You are usually OK with 3.55's, most people, but not all have problems with 3.73's and usually all people hit the limiter with 4.10's. A shift kit will speed up the mechanical/hydraulic process and help but the best answer is to get a chip to 'fix' the shift points.
With gears the part throttle shift points and converter lockup is also changed - you may not notice this, but it IS happening.
We do chips for cars all the time to fix this. A TwEECer will work for this to some extent - but in the higher HP applications there are a number of tranny controls that are not available in the TwEECer software to prevent this from happening.
