Except on paired boards and on the river, I'd avoid half-pot bets. In most situations, if you don't feel comfortable betting pot, then just don't bet.

Q1: I'll bet pot into some straights that hit on the turn when I have a set. At the lower limits ($25 and below), I'm not sure whether that's a good play, though. On the specific hand you're talking about, it's a little tough, too. Against decent players capable of folding, I'd rep the straight a lot of the time if an 8 hit the turn--but I'd also bet out if I had 89JQ or similar. If you're going to rep the straight, I think it's critical that you semi-bluff routinely.

Anyhow, normally, if I got called with a set on a QT7 board, I'd just assume that villain has KJ and NOT bet into a 9 or an A, but I would bet the 8. However, the hand you assume makes KJ a bit less likely and something with J98 more likely. I'd probably bet anyway if I felt like my image was strong and my opponent capable of laying down. But some reads are nice to have when making this play.

Q2: I wouldn't rep a flush without having one with very few exceptions. You can't call pot with a set either. You only have 10 outs. If you feel like someone is taking pots away from you this way, the best answer imo is to check when you DO make the flush (check-call is even ok if it's unlikely they have a set--but bear in mind, you're going to have to call the river again even if the board pairs).

Q3: Bet pot again on the suited J. You still have the nuts.

On that turn, there are now all kinds of draws: low wraps, big wraps, and the flush. I'd always check OOP if any of those hits and the board doesn't pair. But I'm very likely to call if any but the small straight hits (again, reads are nice to have).

Q4: I disagree that 643 is unlikely. If you bet, that's what you're now repping, and, yes, you should be worried about a draw. But that doesn't necessarily mean that you shouldn't rep that hand yourself. I'll bet the 3 on the turn sometimes and sometimes check-fold.

Aisthesis answered your questions already and i think at the most points similar

If i have topset and a possible scare card/Flushdraw hit i will slowdown most of the time and check/ and rethink odds/action on turn and then call or fold if the odds+implied odds if the river pairs are bad.At the long run it will pay me off because im 75% favorite against the flush at the flop with perhaps implied odds if i catch my boat at a flush board against Nutflush that can't let go If you get 3 callers the pot is really nice you can push a free turn which makes me again 75% favorite for a big Pot.Everybody who is calling with a flush or straight draw will pay me off big if he call at long run
But if i call big bets if their draw hits i give them implied odds to make their call right
If the opponents are straighforward i check it against flush.If they are really passive i make a little block bet that don't look weak but that allows me to fold to a pot raise.I call a little raise so that they think i also have a little flush or what and will call a paired river bet/raise more than usually! They won't raise pot without a Nut or second nut Flush if they are thinking because there should be a high flushdraw out there and i could also have it trying suck them in with a weaker bet.But against TAG opponent i check/call/fold because i don't want to pay them off chasing their draws.
I want to get value in when im favorite not when only 30% dog or what!
I put all pressure/pot bet on opponents everytime i have the best of it and that is the flop!If a real scare card hits i no longer have the best of it i try to let it go if i get the feeling the draw hits my opponent which i try to check out for free by checking and calling if it will pay me off at long run through odds.
But if i have Topset and 1 random straight draw card is out there i make a reasonable bet especially when checked to me and the opponents betting their good nearly everytime so i get the feeling they are drawing and don't want to take the risk of getting drawn out because i was way to scared because of the "scare card" and lost much of EV+.
I will push it real hard if i think im still favourite and i think they are still drawing,but try to shut down immediately if i get the feeling that this card is really bad. It takes dicipline to do this but the odds are at your favour nearly all the time.
Best is to have the action on flop that you can checkraise really big so that you are able to push all or nearly all chips at turns that didn't bring the flush Everytime i have to fold to turn action i complain a little to the poker God and please them to get me a little more luck next time because made no fault and did my money as a favorite in and made a good fold which will pay me off at long run That are also the way i can get over the crazy suckouts and beats I think it all comes to EV+ play.And not pushing to a reasonable scarecard is EV+. Wow long Posting. I write to much and should play more to learn and win some $ to get out of the low limits i think