Motor ran well before HEI, but I did a intake manifold swap, new timing chain and lifters in conjunction. Cured my lifter noise. Ruled out anything mechanical, I think the intermittent spark from the timing light coinciding with the crappy running pretty much gurantees this is an ignition problem.
Did you try running that crappy reluctor before filing it? I am curious if this could be the cause of my issue, having a hard time picking up the signal at higher rpm's. Gap varies about 0.05" to 0.15" right now. It was touching on some when i first got it. It had apparently been gapped at 0.08" from the factory, but on one of the shorter arms.