Might be a shot in the dark, but check all your grounds. Especially the ones located at the rear of the driverside cylinder head. When I had my motor out a few years ago, those grounds either never got tightened or worked loose (either way my fault) and they caused all kinds of driveability issues, idle issues, took out an O2 sensor, etc. etc.
If you didn't pull the heads then there would be little reason for them to be acting up, but worth a try.
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1999 Formula 6spd (The driver)
1997 2500 Ext. Cab Dodge 4x4 CTD 5spd (The Earth Mover)
1970 Nova 5spd (The toy)
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