Boy, is that ever a chronology of horror stories.
Yes, a lot of problems have been reported with the new-style plastic mag followers. They were redesigned to reduce the metal followers' tendency to "fountain" when a loaded mag is dropped, and while they did help that problem, they definitely do not feed as well. You should try to buy or borrow some mags with the original metal followers, if only for debugging purposes.
Sounds like you tried all the obvious fixes, so it may be time to start thinking "zebras."
--First off, if the mag-block pin holes were drilled slightly off, yes, it could screw up feeding. You might try driving the pins out and trying one of the one-piece drop-in mag blocks -- preferably one that you know works OK.
--On the odd chance that it's some sort of buffer/spring problem, consider swapping out the collapsible stock for a full-length A1 or A2. You can use the standard .223 buffer for 9mm with a full-length stock.
--Strip down one of the lower receivers and inspect everything. The 9mm bolt design, as it comes from Colt, forces the hammer to impact the disconnector, and it pretty well batters your internals. So look for damage/excessive wear on the hammer and disconnector. Replace with new Colt parts and see if it runs OK.
In particular, 9mm uppers (with the impact problems cited above) frequently break the hammer and trigger pins. Colt uses hardened stainless steel (silver) pins on factory 9mm guns, but yours may have shipped with standard (parkerized) pins. If so, they can snap and, while the gun still runs, it throws off the geometry of the fire control parts.
I would also definitely replace all the fire-control springs in the lower receiver -- hammer, trigger, disconnector. The 9mm setup puts a lot more stress on the springs and they weaken much faster. I replace mine every 5,000 rounds or so.
Hope this helps.