As for the oil leak, that probably wont cause it to run bad unless you are completely out of oil and have been running it that way for a while
The running bad? Well, it could be a number of things. Since is sound good when you are warming it up, it sounds like it could be the catylitic converter. Does it rev up ok? or does it only run bad when you try to drive it? Does it back fire when you rev it or drive it? How longs it been since you tuned it up? I'd also check the O2 sensor if it has one. (not sure because mine is a il6)
Keep us posted...
2004 Rubicon, 6" lift, 35s, winch, hard top, full doors, bumpers, tire carrier and rock sliders.