Your thought process is pretty good. It's all about ranges and equity.
One thing to do is remove QQ+ and probably AK from villain's calling range pre-flop. Also discount A9o. Even ATo is iffy.
If villain's calling range is JJ-22, AQs-A2s, AQ-J, K9s+, Q9s+, J9s+, T9s, 98s, 87s, 76s, 65s, 54s that's still a bit wide, as cold-calling 14% of the time in that spot is a bit too much, although it might be quite typical at 5NL.
The equity calculation will still be fairly accurate nonetheless when you have a decent overpair. If you had AK by contrast, you'd be an underdog on that flop.
The tricky thing is working out villain's continuance range vs a flop bet. I think most players are folding most overcards on that board, although some will float. The turn is a pretty bad card for you, but check-calling is OK because villain can bet with worse, including a bunch of pair+draw combos. You're never way ahead though.
You can do an EV calculation on the river, but it should be a fold if villain bets big.
When you've gained experience of doing equity calculations like this, you can start thinking about not just how you play one hand (like jacks) on this board, but how you'd play your whole range. When you can visualize a whole range, you can immediately see things like "This (wet) flop strongly favours the player in position" and plan accordingly.
You're already thinking more deeply about how to play a hand than most beginners, so that's good.