Maybe flop raise could be a bit bigger looking back but the turn donk shove really caught me off guard. I mean He has nothing else but a better set, 88 or KQs here right?

villain is fairly tight with a 13/9 and 33 aggression factor.

Let's say V raises a 10% range, that flop hits a bunch of made hands (TT/JJ/AJ/KJ/AT/KTs). Your flop raise should have blown out KTs/AT and maybe KJ. On the turn you get a pot sized bet, but V is all in because he was so short stacked to begin with. He actually has quite a bit of his range that's ahead of you (JJ/TT/99/88/KQ = 3%, or a bit under 1/3 of his open raise range), so you could be in trouble here.

That said, if V had JJ/TT on the flop then it was just a bad beat and you should have been happy to lose your money there. 99 had the wrong odds to call your raise (8% chance of hitting his set) but KQ (33%) and even 88 (16%) had enough odds if they could get you to shove on the turn or river (21c to win $1.34 needs only 15% equity to be profitable).

Raising something more like 40 or 50c on the flop would have changed the picture - maybe you would have folded out AJ/AT/KJ but all his pocket pairs probably would have stuck (both the TT and JJ sets, but microstakes players hate letting go of AA/KK), and then you'd be happy to call his turn bet as he shouldn't have been there with his draws anyway and you'll beat him in the long run like that. A 50c flop raise means V now needs to put in 42c for a chance to win - KQ still has the right odds to call, but there's now so much money in the middle and enough hands that he'll call with (big pocket pairs and maybe AJ/AT) that calling his turn shove (which would only be 55c into a $1.21 pot giving you 3.2:1 odds) would feel fine.

Not folding. If you are behind you got outs yo.

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