If you say the plug boots look normal, then I have no idea how water is getting in there. I dont think it can be anything other than condensation. Might want to try a dealer
Unless I'm missing something, the only way water is getting in there is from condensation and not sure how your engine is making so much its causing a misfire.
Your car sounds different from USA models. Is it a foreign model only?
You can clean the PVC valve with brake cleaner if needed. I would check the engine air filter but also cabin air filter too. You could go ahead and replace transmission fluid, there's a link somewhere with a real easy step by step. Theres no fuel filter on this model.
That noise could be sway...