Whew, just got back from the holiday.
An unplugged O2 sensor shouldn't cause surging at idle or stalling, neither will running open header. I can walk out into my shop and unplug every single O2 sensor on every single car, and unbolt the exhausts as well, and not a single one of 'em will surge or stall. You should not let a shop that tells you that work on your car...
Why is your car there anyways??
For the shifting thing (although you've apparently got this taken care of), it shouldn't be anything that you messed with that caused that issue (key word 'shouldn't). Next time it doesn't shift out of park, first get out and make sure your brake lights are working - if they aren't, then you most likely need to replace your brake light switch. If the brake lights ARE working, you need to check this:
Make sure it's clicking when you step on the brake pedal. If it isn't, remove the connector and check for power and ground with the brake pedal depressed with a DVOM.
Now, as far as the other problems, it sounds to ME like you've got either a vacuum leak or a fuel delivery problem. It could be a few other things, but I'm saying this assuming you didn't fuck anything up or misinstall anything when you put the motor in. Check fuel pressure at the rail AND before the fuel filter, and do a smoke test on the intake system to see if there's anything leaking. You can also spray down the engine/intake with brake clean (make sure it's flammable, a lot of places sell non-flammable brake clean and that WILL NOT work) and see if the idle raises or if you hear a 'whoosh' type sound - if you get either of these when you spray the brake clean in a particular area, that indicates that you've got a vacuum leak there.
Did YOU install the motor yourself, or did the shop that it's at install it? And again, why is it at a shop - especially one that's telling you that running open header can cause surging/stalling/rough running?
Actually, what shop is it at? I'm kinda curious now, haha