When you have the intake manifold off - make sure you do a forensic tear down -- look at the gasket area for any signs of a leak... pulling oil or oil vapors into the intake can reek havoc on the O2 sensor...
Also - make sure you're valve spring rates match your cam... overlook this at your own peril (or the cams peril...)
I assume you're using a dual sync distributor? Ingition timing controlled by the ECM...
If you're using Accel Gen 7 ECM - have you tried using the VE table estimator function? Also - if your motor is "similar" to many motors built these days - there are tables / tunes - already loaded with the software - have you looked at any of them - and tried any? They're a good way to get a "base" tune - as far as AF ratio and timing etc and then just tweak the VE's where they may be needed.
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