I was certain he had nothing from the beginning and the plan was to call his 3 bet then check/raise any flop. What do you think? Should I have folded pre or on the flop?

Post BI & structure in subject & OP please. Leave the results out. Post reads.

The small 3bet from Villain really depends on our read. If he's not suicidal, it's usually best to flat(or fold if he raises a bit more) only if we can get away from all non monster flops (AJx,KQT, AAx,JJx) assuming he comes out betting decently. We have a good amount of equity on the bubble & can find a lot better edges as the blinds increase. In other words, you don't want to make a habit of getting into wars big stack vs big stack without strong hands. It's easy to trap yourself with AJ,AQ which is why folding is best vs larger 3bets. If you call, the pot is going to be big & you aren't going to be able to just call a flop like this because you're calling off a huge chunk of your stack. Basically, have a plan preflop based on your read.

If he's insane, flatting PF is fine & then c/r as played is standard.

You played it perfect. You got him to put all his chips in as a 4:1 dog. What are you worried about?