'98 Wrangler 4.0L i6 engine misfiring and running rough?

Did you're check engine light come on? if yes you need to get OBD2 scan to check for codes, timing and sensor readings, There are so many possibilities would suggest that first, will work out cheaper than guessing. May need to replace fuel filter if it hasn't been done in last 36000 miles. Hard to say without checking.