Just got done replacing the head on a 90 2.2. it was tbi but i have since converted to the next gen of fuel injection. I had the same issues before when it was tbi as i do now. Head gasket was leaking antifreeze so i knew it was due. Issue i have is if i punch it, it almost dies and then recovers. Also the idle is sputtery is the best to put it. It starts right up no issues there. While i did hg i decided to change all the hard to get to ignition parts. So it got a new crank sensor, module and both coils. Along with new wires and plugs. All ac delco. Still no change. About 2 months ago i did fuel pump and filter. Is there any way to check to see if it skipped a tooth? I do have access to a scanner that reads the timing the ecm sees. Seems to still have good power. I also changed out the iac, map and tps.

Yes there is a way to check the timing. There is a timing cover that iirc you can get at through the passenger wheel well. Again, iirc, there are marks on the 2 sprockets that should point towards each other as you turn the motor over. I haven't done work on the old 2.2's in quite some time so you may want to verify what I said with your own research or a Haynes manual.

You are correct about the gears but i was hoping there was a way without having to tear it open. Anything on the scanner that would help verify?

Taking a step back, I don't see anywhere you mentioned the cam sensor, did you verify that the cam sensor is operating correctly?

Since its a 90 there is no cam sensor.