Raise the flop to whatever amount you would raise with an overpair here. The advantages of raising here are to start building a big pot vs. an overpair. JJ-AA are going to have a hard time laying down on this board. Also, you want to start getting money into the pot before a scare card comes (overcard to his overpair, 3 flush). The disadvantages of raising the flop are possibly scaring off 99/TT and preventing him from bluffing the turn. Another small disadvantage is making AK/AQ fold the flop when the might have hit on the turn if you just flat call. The advantages of raising here outwiegh the disadvantages IMO.

As for the river here, I don't really like the overbet push unless you have a read on the villain of calling too much. Most decent players lay down an overpair here. I would make a value bet of 500 or so.