I can't confirm where exactly the jack point was, but i would guess it was on the frame since the swingarm has to be free for that operation. As for locking the front wheel, it was not. The bike rests on 3 points (sidestand, jack and front wheel) so it should be stable... Plus the rear is only lifted about an inch in the air so i doubt even if your jack was to let go, that it would be critical (the wheel is not removed anyway).This is the part I'm not sure about. Did they jack up the swingarm (I doubt it) or the frame? They didn't use a regular swingarm stand, did they?...use a jack to lift the rear wheel off the ground and you should be able to take the bolts off and install the new ones, using the jack to align the holes with the new bones...
I assume the front wheel was locked in some sort of wheel chock and they jacked up under the bike near the swingarm pivot. Does that sound right?
Also, what have you found regarding the rumor that raising the rear induces wheelies? (That doesn't sound right, but who knows?)
For wheelies i haven't been able to check if there is an effect or not, i had my GF onboard most of the milleage i've done with the new setup so far...