My first gut instinct is that you have a vacuum leak somewhere, possibly in the intake manifold?? I've seen where a leak there can be responsible for random cylinder misfires.
I tend to think you have a "common" hardware cause like this, rather than coincidentally having something wrong with the hardware on 3 of your cylinders at the same time. You've pretty much ruled that out anyways by replacing plugs/wires/cap/rotor and testing compression.
If it were mine, I would start by doing some vacuum testing and if that didn't show anything, possibly an engine analyzer may help. You can tell a lot about how an engine is running by testing vauum.
99 Cherokee, 4.0 AW4, NP242
Past Jeeps: 49 Willys, 81 Scrambler, 88 Comanche
Without "data", all you have is an opinion!