So I made things worse, kind of.
The pistol is now experiencing a lot of failures to return to battery. Case rim gets stuck on the upper lip of the chamber. It happened at least ten times in the first three mags. So I swapped out the flat wire spring for the regular spring and FLG. Things improved but I'd still get a failure to return to battery every few mags or so.
I tend to think the Aftec is providing too much tension and that I may need to radius and polish some of the edges so that the case rim slides up under the hook easier. I will also try removing one of the Aftec springs and see how that works. On another note, the pistol did pass the 10-8 extractor test with the Aftec installed.
I also had this happen:

I think this can be attributed to the Metalform mags. The Metalform mags are junk, I had one mag that stopped locking back the slide after 18 rounds. Garbage, don't buy them.
I also benched it at 21 yards. Very, very poor. This was the best group I could get out of it. That is a standard NRA B8. I took a 6 O'Clock hold, which I had to do for all my shooting. I'm used to POA/POI with my Glock and at speed I ended up pushing shots high.
So I think I'm done for a while with this little project. I need to further tune the extractor, tune the mags, it needs a new barrel bushing, and according to my timer, a mag well. I've lost interest and time for now. I'll keep it for a next winter project.
Final verdict: The NP9 is not worth the money. Unless you want to rebuild everything in the gun to get it to work. Which pushes the price into Glock and M&P range....plus hours worth of work. With the parts and time spent (on the work bench and ####ing around with it at the range) it would be cheaper just to spend the $2k. I don't have any irrational love for the 1911, so it's back to the G17 for me.