Ok, first of all, you need to establish some ground rules for preflop play, one of them is always open with the raise and most would advice that raise should be same size for every hand you open as i already said same size for AA/Ak and for 89s/67s. Now if you checked the link i posted above and the starting hands chart from PSO (if you didnt find it PM me and ill send you the link to it) you have an great idea what to do in any given situation assuming that you know the table positions.
Now lets talk about your EP AK hand, strong starting hands dont happens as often as we want so whenever we got them we want to gain value from them, this is not happening by limping into unopened pot, its happening by raise, also you dont want weak starting hands to see the cheap flop and outdraw you or connect to two pairs or bigger, so bottom line raise pre everytime you want to play a hand. I dont see why you would put someone who raise into a weak ace hand, without any info about that player, that is just something you don't wanna do he can have anything and he might trying to isolate limper or whatever...
About flushdraws, i don't think that they happen that often as you think you might just have small sample, make sure when you have made hand and there is 2 card of the same suit to bet big, so that if they wanna draw their flush they'll pay more than they should and they'll lose longterm, so for the example if you are in headsup bet potsize on flop if he is drawing, if you have more callers bet even bigger, but believe me if you raised 4bb pre you wont have multiple callers that often. and even if you do believe if you bet good you'll win money longterm.