Can of worms, my friend. How many miles? My '99 4.0 liked to grind a little from 1st to 2nd. I changed the transmission fluid to redline MTL and it helped, but did not completely solve the issue (its 98% better though). It could be the synchros, could be any number of things with your clutch.
My suggestion? Pick up some Redline MTL, swap fluids (make sure to get her nice and hot before draining the old fluid, that helps get the gunk out) and see if that does anything. Not any overly expensive fix and a good place to start.
For me, the notchy feel is all but gone after doing that. I also discovered that double clutching OR pulling the into second with slight pressure pushing away from me helps too. All TJs are different, half the fun is seeing what works for you.