And, since we ( collectively that is) have proven that the CRJ can lose power in both engines at high angle of attack, during high altitude stall or upset, have the engines, inlets, or ignition systems been red-designed to protect against this happening again?
Ignition sistems are irellevant if you don't have enough air to feed the engines. If you want to see how do the inlets designed for high AoA at high altitude look like, take a look at F-15, F-14, Su-27 or MiG-29. Too bad none of them can be converted into 45 seat regional jet. And no shape of intakes would help in this case, as they were blanketed by the wing anyway.
CRJ is adequatly protected from stalling at any altitude by stick-shaker and stick-pusher. They worked as designed but it seems they were overriden manually
It's easy to blame lack of hi-alt upset recovery trainning for the mess these guys got themselves into, but they could avoid it by not flying on the backside of the power curve and that's something I was taught while flying C-150. If you get into plane where you have to worry about mach no, it doesn't mean you can take a break from ol' power required vs power available.