The only way that should be able to affect anything is if the cooler is torqued down so hard it flexes the motherboard and makes something lose contact. Which sounds unlikely to me, but I guess it's possible. How much did you tighten the L9a? The AM4 socket doesn't rely on cooler mounting pressure to ensure good CPU-socket contact (unlike LGA sockets like the ones Intel uses), so you don't need to tighten it down all that hard. If your motherboard is flexing visibly, loosen it up a bit. It shouldn't be possible to over tighten the stock coolers given that they use the stock backplate, so that sounds weird. It might be that you've got a dud motherboard, perhaps a cold solder joint in the socket or some such.
As for thermal paste: just let the alcohol evaporate before applying new paste, which should happen almost instantly.