I think I may have a timing issue. Now there is a noise to go along with the rough running. Going to see if I can get ahold of a timing light before I buy anymore parts. just for the record, I did fix some vac leaks the day after I got it, and I have replaced the IAC after I sprayed a can of cleaner down the TB. I really like this Jeep, it's just drivin me nuts. I now understand the things on the windshields "It's a Jeep thing, you wouldn"t understand" I hope I can figure out the issue before it nickle and dimes me to death.
Timing light really isn't going to do you much good in the traditional sense. The ECU (computer) controls the timing and you really can't adjust anything.
You can hook the timing light up to each individual spark plug cable, shine the light at something dark like the relays cover and see when that particular cable and/or plug misfires. The distributor caps and rotors seem to wear pretty fast on my 88, the plugs seem to last forever.
Weak spark is definitely a possibility, high resistance plug wires or coil to cap wire can cause that. As can low voltage to the coil module or even corroded contacts between the module and the coil. I had all of that going on at one time or another, corroded connectors would cut down on the voltage to the coil, the module to coil contacts were green, my plug wires were iffy and my distributor cap (inside) looked pretty bad. Even the underside of my relay block was green and corroded.
I'd still ohm test the CPS, when they test near the outside of the tolerance around 190 ohms or so, they can act up. Heat can change the ohm values in a CPS. It may only act up when it's hot. Runs poorly, misses, has no power, gets hard to impossible to start.
Be sure and check the vacuum tube from your TB to the MAP sensor. Easy to break or knock out of the TB, there are two holes you can plug it into, but only one goes all the way through the side of the TB, plugging it into the wrong hole can screw up your day. I blow thorugh the MAP vacuum line and the side of the TB where the Map vacuum line plugs in. Screw up the Map vacuum line and your motor is subject idle like chit, miss and run really rich, blow smoke and unburnt fuel out of the exhaust and accelerate slowly if at all.
I never stuck much money into my 88, but have stuck a lot of time into it. It idles and runs better than my 96 now. One thing I did do that saved me a lot of time and money was to get a complete set of junkyard sensors. I compare one sensor against the other, before buying anything. I'm still running most all of my original (22 year old) sensors except for the CPS and oil sending unit.
Re torquing the intake/exhaust manifold bolts is almost a must do thing. Leave the end studs alone, they tend to snap off. Two people, one on the bottom to place the socket and extension on the bolt, one on top to work the torque wrench, is the easiest way I've found, tighten from the center out. Bolts are hard to get to on the bottom and can be frustrating.