31's and 4.10 on a 2.5L is not optimal, but it is liveable. Ideally, you would want 4.88's on the 31's (yeah, I know most sites recommend 4.56, but trust me on this one, as I used to run this combo). The I4 likes to rev up a bit more than the I6, so cruising at 70mph at 3.5K RPM is OK with the little engine that could (you could drive it like that all day long without problems). i now run 33's on 4.88, and I miss the old setup, but again, it is liveable. I just wish I could go to 5.13's, but of course, that means new axles...
As for mods, the best advice I can give you is to check out
www.4bangerjp.com and see what the rest of the 4-banging crowd are doing. Typical mods include the 4.0L TB, TB Spacer, eFan, new injectors (here the TJ differs from the YJ), ignition (so that you can gap at .060"), and from there, you move to more expensive mods such as cams...