04DSGB

I have a 2004 Mustang GT 5 speed. As some of you know I have had a crap load of trans work to my car over the past 2 weeks ( bearings, clutch, shift pins) but it still is not right. Ford has screwed my car up. It will hardly go into 1st gear w/o a fight. It gets a little better after it warms up but not good enough. Ford says this is common when new bearings are put in with worn parts. My car has 67,000 miles and shifted fine before the work was done it just had a whining sound. Are TSBs only good if the car still has a factory warranty? Please help i'm going crazy here. BTW I have a aftermarket warranty.