2004 Rubicon sometimes cannot get in to gears 1st-3rd and if it does shift it makes grinding noises but fourth and fifth gear are fine so what wrong?

Sounds like the synchros are failing. Usually a time consuming fix for a professional. Estimate about $1000.00 for a repair if that's the problem.

Grinding in all but 4th and 5th is an indication of a bad input shaft bearing