Paul to clarify; have you removed the pilot jet and made sure the passage is clear? Additionally when it is missing does it do it at half throttle or full throttle etc? I could be totally wrong but it seems like with the mixture screw reset and now working the idle circuit is ok but as you transition from idle circuit to pilot it starts missing and gets really bad on the pilot as that is partially clogged and then as you transition to the main the problem goes away.
Do some testing to isolate the problem; in 2nd gear with the car at 1200 rpms floor it (the motor may stumble if the accelerator pump is not functioning properly) and see if it misses or pulls cleanly. If the miss is gone at wide open throttle repeat the experiment at 3/4, 1/2 and 1/4 throttle. You can tape blocks to the throttle stop to limit the travel to get the desired setting. When the miss returns note the throttle setting. The pilot jet is in play from roughly 1/4 to 1/2 throttle.
If the car misses at all throttle settings at the exact same RPM then I would start checking the distributor; is the vacuum advance diaphragm got a pin hole leak (disconnect it), use a pair of plug wire pliers and pull a wire of each cylinder and see if one is weak. Do you have points or electronic ignition. If its points double check the dwell.
I'm betting on a partially plugged pilot circuit.........again I could be totally wrong.

Tom