Fill out your Jeep profile so we know what you are driving and can help you. Also, explain what it's doing in a little more detail because what you have described so far could be caused by a lot of things. Was it doing it before you changed the plugs and wires? If not, what brand/type of plugs did you install? Did you check the gap on them?
All the stuff you've done and are planning to do will help it run better. Just don't know enough about your problem to know if it will correct the issue.
I have read hundreds, if not thousands, of threads on here and it's amazing the percentage of problems that wind up being caused by something the owner has accidentally done to the Jeep while working on it.
Moral to the story: If you moved it, unscrewed it, unbolted it, hammered on it, wiped it off, re-wired or replaced it - Check there first!