Did you ever get this figured out? I have it too, but maybe not as bad as what you describe. I have the thud in the rear but also a "rattle" that comes from the large damper on the side of the trans. It rides on a shaft coming out of the trans and moves with every shift. It makes noise because...
Curious if our Bullitt's have this feature. I haven't tried it but probably will after reading this in an article about the subject:
"Ford lovers have long had a factory no-lift shift option for the Mustang in the form of the Blue Oval's Power Packages (PP1, PP2, PP3) available from Ford...
I just had an appointment at a dealer for a similar issue. I've been under the car on jack stands trying to locate the source for a clunking. I found two sources. One appears to be excessive gear lash in the rear end. I can turn the driveshaft with my hand and everything from the trans to the...
It would seem first gear would almost be a granny gear now. I'm sure starting in second gear is no problem now. If I may, what did the gear change cost you?