I'd like to know the details of the "output shaft being out of tolerance". Gears loose on the output shaft? Too much difference between the gear(bushing) ID and shaft OD? To me more likely too much end play on the gears and could very well indeed lend itself to a popping out of gear problem. The side to side clearances on the output shaft gears need to be checked and adjusted properly to keep everything kosher.
No matter what, Rob's problems with AA are troublesome. Personally I believe the Orion setup is a great way to go provided that the parts kit contents supplied by AA is accurately machined and complete with everything you need.
Yeah I'm just parroting back information at this point, but I suspect it's clearance between bushing and shaft, based on what I'd read. Either way, one thing I absolutely will say is that nobody has been complaining about AA's customer service - seems like they're at least trying to resolve these issues.
For those who have built them - is there substantially more "setup" in these cases? when I rebuilt my 4-speed case I literally slapped it together with new bearings, checked a couple of preloads, confirmed it shifted, and tossed it back in. So far, no issues.