Opponent is both loose and has a wide variety of preflop raising hands. I also saw him call a big raise preflop with KJs to call a pot sized all in on a flop of A9x (none of his suit)

Party Poker No-Limit Hold'em, $0.5 BB (9 handed)

MP2 ($13.2)
MP3 ($47.06)
CO ($39.68)
Hero ($49.25)
SB ($31.39)
BB ($56.03)
UTG ($92.45)
UTG+1 ($58.46)
MP1 ($35.17)

Preflop: Hero is Button with , .
UTG calls $0.50, 4 folds, CO raises to $3, Hero calls $3, SB calls $2.75, 1 fold, UTG calls $2.50.

Flop: ($12.50) , , (4 players)
SB checks, UTG checks, CO bets $3, Hero raises to $9, SB folds, UTG folds, CO calls $6.

Turn: ($30.50) (2 players)
CO checks, Hero checks.

River: ($30.50) (2 players)
CO checks, Hero checks.

Final Pot: $30.50

Results in white below:
CO has 7c 7s (one pair, sevens).
Hero has As Ks (one pair, aces).
Outcome: Hero wins $30.50.

The flop bet just seemed so weak that I raised it up. He thought for a long time and finally called. I took the free card and hit my A on the river but it completed the flush and he could now have two pair with AJ so I took the free showdown. Was this raise on the flop a good move since I only had the overcard outs? Should I have followed through on the turn?

He would need AJ to have 2 pair, not AQ. Not too many people will raise to 6BBs with AJ and then only bet $3 into a $13 pot when they flop TPTK, so I would right that hand off.

I dont think he has the flush either or he would probably bet the river. Having said that, I probably wouldnt bet the river either.

yeah, typo on my part, i'll correct that.