First off, stopping being so hard on your self, you live, you learn and get hugs. It is said that NLHE takes minutes to learn a lifetime to master. So ease up a little.
Two, your KK fold was likely to be a bad move given all the information, you can't always be afraid of a raise or LAGS are going to eat you up.
Three, your QQ was a good fold, again based off what information you provided. You limped with QQ ( I would wack you on the nose with a paper if I could ) and because you limped you let the small hands in for cheap, any small pair is very likely to limp in.
And given that the villain limped shoved, it just screams set. At best for your situation your villain would have 910 or 45, maybe even limped with 86 ( suited one gappers not uncommon to be limped by loser players) and your fading a draw. But like you said the only hands your beating here are Ax to the board and all none set small pairs, JJ-99,77,33,44. And he might have even been trying to be clever and limp AA or KK ( especially if its a low buy-in tournament with lots of fish )
So the summary of hands your beating vs hands your not, a fold was a correct play. Plus the blinds where at 50/100, so there is still plenty of tournament left to pick a better spot with.
PS....what you have learned about limping QQ? yeah, that's why we don't do that..lol, I limped AA once and got cracked off by 24 in the BB, I rarely limp those anymore...