extremely soft 2nd to 3rd shift

If the cable isn't pulling the lever on the trans. all the way the shift will be softer. The farther it pulls the lever the higher the throttle pressure and the firmer the shifts. But at the same time it also raises the speed at which it shifts when you adjust the cable to make it pull farther so you have to balance it out between how firm you want the shift and at what speed.

They charged you $2500 to rebuild your trans? That's freaking outrageous unless it had blown up and they had to replace nearly everything!! Sounds like a bunch of crooks that don't even know what their doing.