I had the same tiing. Only rough at idle and at cold start it was fine 'till it changed loops. Did all the same stuff you have done. Tested the MAP sensor and it was good but decided to put one on anyway. Took 85% of the rough out of it. I addea octane booster to the mix and no it is as smooth as it should be. Just remember though, no I6 idles smooth as glass.
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Just got a 1989 YJ too!