Aluminum shafts have to be milled out if you have tried everything else. When they corrode they expand beyond belief and are impossible to remove any other way than in a mill or super heavy duty drill press. The smaller shafts in the rear arms arent as bad to mill out. The aluminum shafts just, plain suck.
Hey Nick, dont feel bad about your purchases. Just be glad your not one of the poor ba#$ards that bought or will buy one of the $600-1200 Exciters that look a hell of a lot rougher than your project. 90% of the exciters on craigs list are junk, or junk by means of being way over priced. Most of what I see are in actuallality $150-300 sleds. Unless you have a super show room condition (or damn near) Exciter SX, there is no way they are worth over $1,000. Im sure you understand this as now you know what it actually takes to make these things decent, reliable machines again after you factor in the cost of purchess and parts.
I have bought many exciters over the last 10 years or so and 99% of them had bad mag side crank seals. Some didnt run, some ran on one cylinder due to a melted mag piston due to a bad mag seal. I have never seen a lean condtion on the pto. The mag side is always the bad one.
Good luck with your project. Holler if ya need anything.