In an 89 YJ some of the things that you mentioned like changing the gas filter is one of the first things you do when you bring it home ,,, A tuneup will help but if the gas filter was that bad then you have a lot of crap in the gas lines .. I'd flush the whole system and take a good look at what comes out .. YJ's are infamous for haveing problems with their carbs because of the dirt and crap thats in the tank ... My wifes 89 4.2L with the Carter Carb was a real pain until we changed it to the Webber Carb.....You mentioned something about it haveing fuel injection which i didn't think an 89 came with unless they had it in the 4cyl. for some strange reason... and if thats true then your jets might be clogged .....