Odd.
I really figured the new mag spring would have fixed it. Swapping back to a standard style stock was a good diagnostic move on your part.
Trying different brands/kinds of ammo might help, it could be a dimensional problem with one particular brand/lot of ammo. But if it does it with everything you run through it, then there is almost certainly a problem with the gun.
I know you said you gave it a good cleaning. But just to be sure, and to humor an old phart, please try this:
Field strip the gun (that is, take off barrel, pull the action bar assy/bolt and slide out, remove trigger plate assy, mag spring and follower) and really wash out the recesses behind the shell stops on both sides of the receiver with whatever kind of spraycan goop you have handy- WD-40, gun scrubber or plastic safe brake cleaner, then promptly blow the recess out with compressed air (use 'canned air' as for computers, with the straw, if you don't have access to a compressor). Pay particular attention to the left side shell stop recess, the one on the other side of the receiver from the ejection port.
Don't try using a brush, and don't get heavy handed with the shell stops when the trigger plate assy is out of the gun. Just spray and blow it out as much as possible as best you can, that will be enough to answer the question of whether there's enough crun in the way to interfere with the shell stops. Don't remove the shell stops, they are staked in and need to stay staked, but a spray'n'wash shouldn't dislodge them and should get rid of anything behind them. If you didn't take precautions to keep abrasive/metal chips/filings/etc. from going down the magazine tube while you were Dremeling out the dimples, a lot of crud could have wound up in the recesses behind the shell stops. That's why I suggest that people pull a rag tied with a string partway through the mag tube from the receiver when doing this operation, then pull the string all the way out the front of the mag tube when they are done, to block the tube then sweep out the trash.
If that doesn't fix it I don't know what's up with this one, could be wear or damage on the action bar assembly, likely the left side. If you have a spare or another gun you can swap parts with, try swappng out the action bar assy. If you don't have another action bar assy you can get hands on and don't know anyone who does have one handy you can use, then PM me and we'll see what we can do.
If that's not it, then it sounds like it could be narrowing down to the shell stops themselves, perhaps most likely the left one. But first try the ammo swap, then cleaning the shell stop recesses, then the action bar assy swap, and let's see what happens. One step at the time...
lpl/nc