Rick,
If you could set the ignition at TDC it would be much simpler. Unfortunately, you have to set the air gap and timing with the piston at the ignition firing point, which is before TDC. I've set them many times. It's an easy procedure but you do need a dial indicator to do it properly. CPS sells a dial indicator for about $90. Much cheaper and just as accurate as the Rotax indicator. Hardest part of the job is getting to the pickups. It involves removing the magneto cover and the rotor and sometimes this means removing the engine to get at them.
Often with two cycles, you will get some loading up if you advance the throttle rapidly after slowing down. It's just the nature of the beast.
Bill.