At just over 6' tall and with a friend holding, I was able to access rhe roof from a 6' step ladder (I'm a MR transit guy). I taped cardboard to the roof with an aperture at the point I wanted ( like open heart surgery). I cut from above, using my Bosch jig saw set to minimum orbital action and a lower speed. The fine tooth metal saw worked fantastic. I too thought of using a pneumatic "nibbler". At the end of my machinations, I just cut the darned hole. Today, I'm going to try to plug it!
I used Hein's adapter to locate and draw the position relative to the two roof corrugations and drilled an 1/8" hole from the inside corresponding to the edge of the rib I wanted as my longitudinal datum. I clamped the flange adapter to the roof with 3m 5200 and let it sit for 24 hrs.
The ac unit on the high roof sounds pretty challenging! How about some rental scaffolding? Two towers and a walkway above...