From what I got from talking to him on the phone, the jams are rounds stopping against the feed ramp or less often a stove pipe.
The movement of the guide rod is as you described. It just comes slightly out of the assembly notch. I didn't know that holding the trigger down while removing the slide made a difference with the NY trigger mod. Learn something new everyday.
I'm meeting up with him tomorrow afternoon to hopefully resolve this issue. He's a nice guy and has done a ton of buying, selling and trading on our local gun trade site. It's a good group of people and I just want to make sure he's getting a fair deal and so am I. I'm not gonna leave the guy with a poorly functioning glock.