The second hand was played about as well as it could be since you were now short stacked and already HU vs UTG2 so all-in was as good a tactic as any and most likely after the flop anyway.
Jason already gave a good analysis of the strategy and tactics for the first hand but I'd like to turn to the psychology aspect when playing an opps such as the one you had in this hand. I play mostly Limit ring games and passive players limping and tagging along with monster hands are actually more common there than I'd expect to find in a NL tournament but learning how to play them would be about the same.
How to play INTO them vs playing AFTER them is slightly different but your thought process is about the same. If your leading into a field of limpers and pre-flop raise callers, or as in your HH case just a single opps, and they just call versus fold or raise, take note of their position, and how they bet coming into the flop and try to determine whether they are on a draw to the board or may be smooth callimg to the turn. Does the board support a drawing hand and is that draw consistant with the position the opps is playing fom? In your HH, your opps called to a

from MP after calling your $400 pre-flop raise - what hands from MP would call the pfr and your flop opener (1/2 the pot) and still have interest in this board/pot? Other than a possible flush draw to high suited connectors, the board doesn't look like a good one for a hand calling my pfr from MP so by calling the flop opener, he's either on a flush draw, looking for a set to a mid pair or smooth calling me with an overpair. The learning curve here is to get more suspicous of callers than raisers. Raisers (and check-raisers) are declaring rights to the pot whereas callers (and check-callers) aren't giving you much info at all and so must be treated with suspicion. Often callers will risk the turn card improving your hand just to milk you for another bet - is that a possibility here?
On the turn (and this is where I'm still working on the best tactics to use), playing AFTER a passive player is generally easier than playing INTO them. If as in your HH the turn card looks like a threat such as the

making a flush did, you are faced with a tough decision.
If playing INTO your opps, do you lead out with a bet or check? Leading out indicates your either blind or aren't afraid of the flush while checking indicates weakness and opens you up to a possible bluff. Whereas, if your play AFTER the opps, you only have to worry about the check-raise.
Normally, I prefer to keep the pressure on (by betting) in either case but if you're dealing with a passive player, the pressure of losing a bet (and the opps fear of giving up a free card) might be the best tactic. Here with the

, you could have checked into MP and see what he does. If he checks thru, he's still got to be on a draw (and just got a free card) but if he bets, you now have to decide whethers he is ahead of you or behind. You can now re-raise or fold (or call although I don't like this much in NL).
If playing AFTER, you could check-thru giving the opps and yourself a freecard but possibly more important, you have removed the check-raise and forced him to lead out on the river if he figures to be ahead. If he leads out on the river you can call it down or fold and if he checks again you call raise him out of the pot or get another bet if he calls.
In either scenero, you are giving up a bet to save a bet (and in a tourney that may be more important than in a ring game) but are risking a free card. Once you have spotted these players, make a entry in their note box that they are calling stations and will limp and/or tagged along with raising hands in case your run across them again.
I welcome comments on my thoughts regarding this tactic for passive players smoothing boss hands.