i'll disclaim that i've never played an MTT, but have played a lot SNG's

Part 1

with your 9's, i would have bet the flop harder. not knowing what his other card was or his stack size, it's hard for me to say whether he would have folded. but on the flop, you had the best of it, yet a vulnerable hand, especially to overcards. since he minimum bet the flop (600), i would have come over the top with at least 2400 with the goal of ending the hand there.

Part 2

this one's tough - even though it's weak, with the board paired, i would have checked my AK and folded to a bet. i, like a lot of people, am really developing a love/hate relationship with AK betting as you did, at least respect his reraise, and fold.

i've really tried to get myself away from the idea of "pot committed" - either i think i can win the hand (either with my cards or bluff/aggression), or get out. i'd rather have the "chip and a chair" chance to come back than throw the rest of my chips in just because i've already bet so much.

my 2 chips.

also forgot - welcome to the board!