If I read correctly you have done:
Tune-up and valve adjustment
Checked for vacuum leaks
fairly new O2 sensor
new cat.

The only other things could be timing, leaking injectors, leaking cold start injector, it could be the cam but I am not sure.

When you tightened up the exhaust manifold and down pipe connection, did you replace the gasket, or just tighten it up? You could still have a small exhaust leak that is allowing fresh air to be drawn into the exhaust and causing the O2 read lean and the ecu is richening the mixture.

Is it failing at both stages of the test, idle and highway rpm's?

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed