Weird engine problems

I have a 88 BII with the 2.9, 5 speed and manual hubs. When I got it in February it seemed to run good except for an occasional tick and a spot it would run rough half way warmed up. It seemed to run good cold, and when completely warm but not in between. It had just been tuned up so I looked for vacuum leaks and checked plugs, wires, cap and rotor, and even changed the fuel filter twice. It just seems to be getting worse and am now at a loss. Could the coil, control module, or even the distributor be the cause? it runs terrible until about 2500-3000 rpm then cleans up and runs good.? Any ideas The other thing with this weird intermittent lifter ticking. It can be one or sometimes multiple lifters ticking, and then it goes away for a few seconds to a few minutes and then it starts again. (Wishing for a simple answer) LOL Maybe just need a 4.0 transplant to save the day. Any help would be great thanks

Have you checked for codes?
You've several sensors that work together that could cause the running issue.
ACT, ECT, MAP, O2.

A bad TPS might make it do what you seeing.

Cheap things you can do: Test the sensors (search online for how to test them), clean the ACT, IAC, and throttle body.

Run some fuel injector cleaner through the engine and see if that helps.

Ticking; these engines get dirty and oil flow through them isn't the best. Run as light an oil as you can without issues, to get better flow. An oil flush might help, I did that on an old BII and it cleared up the tick. On my current BII I had the tick at start up all winter, as soon as it hit 70 degrees it stopped. I had been running "high-mileage" oil and some Marverl Mystery Oil in it for about 300 miles before the tick stopped. warmer temps or the high mileage oil with the MMO added, I don't know which made it stop ticking.

Speaking of MMO, it can also be used in the gas to clean injectors.

Are you using OEM plugs and wire? Can i ask how did you check if they are still ok? It looks like an ignition issue most likely a slight misfire.. When i check the spark plug resistance, i usally do it 1. when normal 2. Apply little heat. Same with wires. Streching it a little bit to see if they lose resistance.