Aloha - I have been having the same problems. Although my trans is still accetable. I believed its cased by a few things.
1 - Engine is slow to drop RPM to accomodate a shift
http://dodgeram.info/tsb/2004/pdf/18-017-04.pdf
2 - Standard Trans is crap / Shifts poorly- Thats why they replaced it this year this with the 6 speed
3 - My XJ had the foreign 5speed (french??) Great shifting trans - We are just used to a an easy shift -
so we forced the shift wearing down the syncros on every shift. Unless you double clutch as I do at times.
and almost always double clutch on a down shift to perform emergency accelleration.