I prefer to bet the turn for value. It's low stakes and cause you bet the flop they may think something like. "So you bet the flop and now you're telling me you have a ace, not sure I believe you". Also you have a solid value hand and he may have floated with an ace high hand that's worse. You will be amazed what players will show up with when calling. Betting allow you to get max value for your hand because of the exponential growth of the pot by the river. I'd bet most rivers as well. In this case it wouldn't have worked out but very unlucky river card given his hand. Now if we get raised on the river large I'd just bet/fold against a player who is generally very passive.

Also I like just checking flop a decent amount

when you cbet flop and turn is one of best card you would like to bet again, checking is alright but higher EV I assume is to bet again. Villain beat you only with 6 combos (sets) + some weird AK(4), and we don't block Kx which likely call turn bet.
As played, river is fine, he represent only 99 and few slowplays, his sizing is strong but vs unknown I'll be calling(pot odds: overvalue worse, or spazz)

not sure about flop bet but think its ok to have some protection.
After flop bet u want to bet the turn around 40% to make villians K/x range to call.

I think flop cbet is fine, given villain's fold to cbet isn't very low. Board is super dry, pot is Hu, we should be supposed to cbet close to 100% of hour range.
Once you have 2 pair there's no reason not to try to go for 3 streets of value.
As played river is a fine call I think

The flop cbet seems meh 3 ways.

On this Ace on turn i didn't see many worse hands which calls, only some flushdraws, 66, A4s.
I think that opponent hasn't too many Ace in his range after calling cbet, so I decided to check.

If you feel this way, I hope that you're bluffing basically all non showdown value hands on the turn.

Given that you don't block any of his Kx I definitely think that you're going to want to keep betting the turn though. If you want to mix in some checks with strong hands to protect your medium strength hands, I would do it with hands that are stronger and that block villain's calling range. Hands like AA and KK might be good candidates to check here for those reasons.