What you're describing sounds like "reversion" and my Vorteched '96 Cobra had it bad with an 83mm Pro-M meter, dual Vortech Mini Race Bypasses, and AFM Power Pipe.
The Power Pipe was even modified to take the outlets of the bypass valves and exhaust them just before the rubber elbow that entered the blower. Still, enough air went backwards through the MAF that it caused surging on the highway and really bad bucking at low throttle settings (like trying to follow slow-moving traffic).
I put in an 85mm Abaco MAF, and the problem went completely away.
Before you get excited, my first Abaco failed completely on the dyno while tuning was being done, and was replaced under warrantee. The second meter also failed but was able to be reprogrammed and seems to be OK. It's like it just lost its programming. I'm not impressed with the reliability which is frustrating since the meter performs so well with regards to driveability.
1996 Cobra Coupe, #7312/7496 black/black
- 522hp/442ft lb (DynoJet 424xLC2)
2001 F-150 Lightning, #1856/6381, red
- 375hp/443ft lb (DynoJet)