Edit: TL;DR : If short-stroking, do it from the pick-up side.
I'm retarded too, haha, let me explain in details.
Removing teeth both side can screw the tappet timing. Removing from the release side of the sector gear will release the piston before the tappet is fully extended. That sucks. Removing from the pick-up side
could lead to the tappet being picked up and pulled back before the piston finished it's stroke
(which would normally cause premature engagement if the teeth were still present). But that's less likely, so that's why we recommend removing from there.
So, the guides are right, but only to a point.
On both cases, you will lose power but will still shoot a BB.
Myself, I got confused by lurkingknight's post, and I'm really sorry for this. Nothing I hate more than giving false information.
About the nozzle not at the same place after full auto, that's perfectly normal.
In semi auto, the cutoff lever is activated by the sector gear revolution, so it stops at the same place every time. Since in full auto the cutoff is not engaged, the cycle will stop where you release the trigger. And since us human cannot release the trigger at the same place every time, the nozzle will stop at random. Like I said, not a problem
Does the gun feed with a weaker battery?
If yes, the nozzle, when at full speed, is too quick for the BB to get up and chambered in the hop-up chamber. A sector clip will help, as well as better mags ( don't know the EMAG, but if they're genuine PTS they should feel ) or better BB (* bioval should be okay, but try something else just to eliminate that variable ).
If not, I'd look at the nozzle itself. Maybe it's too long, so even when fully retracted it doesn't allow a BB to get in. Flip the rifle around, point a flashlight at the BB feed path, and shoot with a low powered battery so you can see the cycle. If you put a BB in there, it won't feed if the nozzle is too long.