Clunking when i shift

This mysterious clunking.... Every time I shift gears, doesn't matter which gear or how fast I'm going I hear a sick clunk from my rear end area. I just replaced my tranny fluid, and I had no metal flecks or anything to tell me something was wrong with it. I replaced my rear pinion seal, and although I had lost alot of fluid there didn't seem to be anything wrong with it. I go to school for auto tech, I can't figure it out, and neither can my instructors. Wtf is going on? must be rear differential right??? It's a 97 GT. Please help me it's driving me nuts. Another symptom is me having to wrestle to get into gear sometimes, and i see no clutch or tranny problems. This might just be the way mustangs are though.
:shrug:
 
Was the noise there before you changed the pinion seal? If not, I would suspect that the pinion crush washer may have crushed quite a bit more when you tightened the pinion nut. This would completely jack the backlash that the rear gear should see. This could easily cause a loud clunk since there would be so much play in the gears.

Also check your U joints. A joint going out will cause banging noises. It will also usually cause a vibration at highway speeds.

Check all the rear control arm bushings. If one or more has deteriorated and come out thenit will allow the rear end to move around to much.

Check those things and see what you find.