I'm glad they got it to work well with your canon lenses... Regarding the AF board... a year/year and a half ago or so I sent in my 7d and 17-40 in to be cleaned through CPS and asked for them to double check focus to make 100% I was getting the sharpest images with the lens, might as well... When they came back, the camera was notated that it was within specs however they said there was an issue with the computer chip with the 17-40 and they replaced it/fixed it for free. I dont recall bad focus before i sent it in, i just wanted to double check it, however it is fixed and i haven't had problems since. Regarding the computer chips goes, (AF chips), computer techs treat electricals with gloves and sterile environments, however we, as photographers, aren't nearly as protective of our lenses (especially the electrical contacts) nearly as much. That being said, I'm 100% confident the contacts are protected to an extent to account for this.
Your 50mm 1.8... is that a metal mount or a plastic mount? I've heard of the AF motor frying.... the 50 1.4 is infamous for that (for people who shoot constantly with that lens)... and that lens is almost 3x the price of the 1.8. So... given that, with this lens I wouldn't be as concerned as I would if it happened to my 17-40 or 70-200, etc...
Lastly, I wouldn't lose sleep over the turning off your camera when changing lenses, etc... I dont do that, but then that could account to my 17-40mm never mind.. haha. But then again I haven't had problems since so who knows. Use your best judgement. If you're in a dry climate with a lot of static electricity, then by all means... if you're in a moist climate, then maybe not so much... You know denver better than I do but keep us updated as you see fit. Keep in touch with your ventures.