You didn't have any problems before doing the tune up? Are there any other symptoms?
If it was running fine before I'd start with the things you messed with in the engine before going elsewhere.
1) check the spark in each plug. You can do this easily by turning the Jeep on, letting it settle to its idle, and then unplugging the spark plug. You SHOULD hear a drop in the RPMs. If you don't get a drop for one of them pull it, ground it, and have someone turn the engine over to confirm.
2) what kind of spark plugs did you use? YJs love cheap and tough spark plugs. I use Champions and get pretty good results.
3) when you were working around the engine you could have accidentally pulled a vacuum line. An early symptom of this is its running rich and idles higher than normal. If so, Google Jeep YJ vacuum schematic and with a can of carb cleaner just spray around each connection. If there is a bump in RPMs you've found a leak.
Engines need fuel/air, spark, and compression to run well. I can't imagine it's compression if it was running well before; I'd start with the above three!
