Ok, ive got an 03 tj with a 5 speed, 40k, 3in lift and 33's, just had new 4.56's and a lockrite in the rear installed and when driving it home today, shifting from gear to gear there was slight grinding (nothing too terrible) from 1st through 4th and 5th was fine. it wasn't so bad if i took longer to go from gear to gear, like i was driving an old pickup. I was wanting to know if this type of thing happens since you just changed to axle ratio's and all or is it something thats gonna end up having me re-build the tranny? Im a noobie to stuff like this, so any help is greatly appreciated.  

Sounds like the synchro's in the tranny. Mines doing the same thing.  

yea but the tranny was just fine before i had the 4.56's installed  

still kinda sounds like the synchros, mine does it in all the gears, but mine just started a few thousand miles shy of 240,000 miles. shouldnt have anything to do with the axles. must have been the gremlins waiting for your jeep to go on the rack to get into the tranny!  

Its one of those things happens and then you start looking for something that caused it. I had the slave cyl replaced in mine and then the synchros started going out. That was about 5k miles ago. Like jeep 420 said, doubt its the gears.  

When was the last time you changed your oil?? I know It's been to long when it starts to get hard to shift, you might try it!  

i'm having a similar issue in a 2002 tj.  i can shift smoothly; however, when i shift i feel and hear a large knocking sound under the rear seat.  any suggestions?  

rear universal joint on the driveshaft maybe??  

x2 on the u-joint also check the tranny mount.  

I agree with the Synchro comments. I am on my second AX15. Replaced just 2.5 years ago. Rebuilt, not new. Synchros are starting to go again. Last time I waited until shifting became too difficult to tolerate before I replaced it.
Next time I might bite the bullet and go for the NV4500 upgrade with an Atlas II 3.8 T-Case from Quadratec.