Mine has done this since day one. Not regeared. 1st to 2nd and 2nd to 3rd are the worst. It's almost as if it gets caught up on something. I've always assumed it was normal and wrote it off as it being a jeep and not a sports car.

 

Someone else here had this issue after changing out his clutch, and it turned out be be an issue with the clutch binding slightly and not releasing fully resulting in the transmission always receiving some torque from the flywheel and making gear changes difficult. I cant remember whether it was an allignment issue or something to do with the installation of the throwout bearing but apparantly there's something tricky involved when installing the JK's clutch that can cause this (I'm pretty sure it wasn't the slave cylinder, however these slaves are known to play up and require replacement after clutch changes).

The fact that it's suddenly happened immediately after you changed out the clutch discounts suggestions that it is just the normal notchiness of these transmissions that can be alleiviated with different gear oil. If it's just the slave then no worries; 80 bucks and an hour or so of your time & you'll be good to go. Otherwise you may need to drop the trans to check for the allignment and installation of the clutch disc, pressure plate and TOB.