I think my problem was as simple as cleaning some connectors. Yesterday I used electrical contact cleaner to clean the AFM plug, head temp sensor, reset the ECU and cleaned all the plugs. Tightened up all the hose clamps also. Drove it hard through 3rd getting on the freeway and didn't feel any stumbling. Never heard the suggestion of taking it out for a long drive after reseting the ECU but out of coincidence I drove it on the highway for 30 minutes. Today I took it up to about 5400 rpm in 3rd and still didn't feel any stumbling. I don't seem to be getting the puff of smoke I used to get when flooring it.
Now I'm pretty sure it was a problem with the AFM or the ECU or I hope thats all it was. We'll see how it holds up.