Personally I would jam because he looks terrible and I've seen stranger things than villain calling off everything with a flush here. Even on this board fish can look at objective strength instead of relative strength and just think, oh well I have a flush and that's a good hand isn't it?

It's a key point that he did call with a 9 high flush, so it's almost certain that you could have got away with more EV. How much more is difficult to tell, but I would always lean towards trying to get his stack, just in case.

I think the raise is fine. You jam he folds. This looks like a flush so raise to get paid by a flush.

At river you have ~ $21 into $6.35. They lead for $3 you make it $9.50 to get $6.50 in added value. If they call more than 1/3rd of the time to a shove as they do to the $6.50 you should shove; 6.50:21 is close to 1:3. I do think as high as 90% of the time you shove river they fold.

I hope that makes sense.