Jeep Misfire... Looking for Diagnostic Software

So I'm tracking down a multi-cylinder misfire on a 1999 Jeep Wrangler 4.0L. I just bought the vehicle and it was in sad shape. I've thrown some parts at it (all the usual suspects: full tune-up, CPS, TPS, distributor pickup, injectors and connectors, fuel pump, O2, cleaned the throttle body, flushed fuel lines and rail, fixed countless vacuum leaks... it needed the TLC) but I'm still getting a misfire at all RPMs. I even tried some snake oil (seafoam combustion chamber cleaner) on it because these engines are known for carbon buildup on the exhaust valves.
After all that, the misfire is less severe but it's still there. Handheld scanner shows no misfire counts but I can hear it in the exhaust and feel it on the butt dyno. It re-sets the codes after 10-12 miles of driving.
So before I pull the manifolds and visually inspect the valves, I'm hoping to find some software to see what the ECM is doing or thinks it's doing. I have an OBD-USB cable, so I'm just trying to find some good, cheap (free?) software to monitor engine function.
Any recommendations? I have ForScan for FoMoCo vehicles but pretty sure that won't work on Chrysler stuff.

Thanks!

I can't guide you to any software, but just to give you another base to cover...

Which handheld scanner do you have? I can make some recommendations, but they may not be better than what you already have. :silly:

Which codes reset, exactly?

I second pole71's recommendation of a cranking compression test, given the engine and the work already done. A power balance test (by unplugging injectors) would be another good option to pick out a weak cylinder.

The Bluetooth dongles sold as ELM327 work fine with Android phone apps OBDautoDoctor or Torque. If you want a hand held scantool Autel and Launch do entry level tools a a good price on Amaon or ebay Something like an Autel AL519 or Launch Creader VI might suit.
I also would advise you should some some kind of compression test before ripping the heads off