Welcome to JF...
Do some searching on the forum... there are countless posts on the problem you are describing.
Most ppl agree that the roughness is pretty "normal"... my nv3550 does the same thing. Its a truck tranny and not a sports car tranny after all.
That said... depending on how bad it is, you may need a new clutch, but with as few miles as u have I doubt it. You can also try changing the fluid... some ppl sware by royal purple, some ppl say to stick to the Mopar stuff.. again, a search will net a lot of good results.
When I bought my jeep (200k+ mi) the shift was pretty bad.. almost a grind there. So I put in a new clutch and changed the fluid. The grid went away and it got a lot better, but it still had the roughness you describe.... runs perfect, just rough. Aka welcome to jeep ownership LOL.
"Some may never live, but the crazy never die."