Heads Up Home Game - Advice

Ok, playing a pickup tourney of three people $1,000 in chips. After 1/2 hr it was down to two people. I, Hero, had about 58% of the chips, approx. $1750, to Villain's $1250. Villain is a good player and will raise/all-in with 88-JJ, and just raise with any high cards. Oh, and blinds were at $50/$100 Here's the hand:

Preflop: Hero is BB with K [img]/images/graemlins/diamond.gif[/img] , 9 [img]/images/graemlins/club.gif[/img] .
Villain calls, Hero checks.

Flop: K [img]/images/graemlins/spade.gif[/img] , 9 [img]/images/graemlins/spade.gif[/img] , A [img]/images/graemlins/spade.gif[/img] (2 players)
Villain checks, Hero checks.

Turn: 3 [img]/images/graemlins/club.gif[/img] (2 players)
Villain checks, Hero bets $300, Villain raises all-in, Hero calls.

River: J [img]/images/graemlins/spade.gif[/img] (2 players)

Villain showed 5 [img]/images/graemlins/club.gif[/img] 2 [img]/images/graemlins/spade.gif[/img] . We discussed the hand afterwards and he said that he had a read that I had TP or Two Pair and nothing to do with the flush. I knew he didn't have the flush because he would have bet the flop with a draw.

Should I have made a strong bet on the flop and taken down the blinds?

Or was my slow playing to make more correct and just a victim of a bad beat?

I'm trying to improve my game and any advice is appreciated.