Verse 15:22 "And We send the winds fertilising, and cause water to descend from the sky, and give it you to drink. It is not ye who are the holders of the store thereof."
You said about this verse, "Winds only indirectly influence the formation of rain...".
Okay, now keep in mind what I said about allegorical verses and the Quran not being a book of science. Technically speaking, even when I say "clouds give rain" it is false. It is dust on which rain droplets condense due to electromagnetic interactions and then they break free from mutual electromagnetic attraction due to gravitational forces when they get too heavy etc etc. My point is, that the winds cause clouds to form is a good enough statement.
Verse 16:68 talks about how God created bees to take habitation in places like mountains, trees, and human dwellings. It uses the arabic word for "bee" which encompasses both male bees and female bees.
Verse 16:69 continues and says how God created the bee to make honey, but in this verse, only the female bee is referred to, not the male bee.
As we know, only female bees make honey, not male bees. So this is another big sign that the Quran is really from God, after all, who knew at that time that it was female bees that produced honey? Of course you could chalk this up to a lucky guess... but what about all the other "coincidences" in the Quran then?
(The following is one of my favorite verses)
Verse 21:30 first relevant part: "the heavens and the earth were enmeshed then we unmeshed them both"
We know today that about 5 billion years ago the earth and the solar system were one cloud of gas that was condensing. If we go back even more, our galaxy was a big cloud of gas that was condensing, and if we go back even more, the whole universe was a big cloud of gas that was condensing. This verse clearly refers to the fact that the Earth separated from the rest of the universe ("the heavens"), as if they were joined together, and now they are differentiated.
If you still have doubts as to whether this verse really refers to the primordial solar system gas cloud, then look at this verse which explicitly mentions the gas cloud:
Verse 41:11 "Then turned He to the heaven when it was smoke, and said unto it and unto the earth: Come both of you, willingly or loth. They said: We come, obedient."
"when it was smoke" clearly refers to the gas cloud, because as you know, when you look at gas clouds from far away in space, they look like smoke (we have pictures of thousands from telescopes similar to what our solar system must have been like 5 billion years ago).
Verse 21:30 second relevant part: "and we created from water every living thing"
The word in arabic used for "created" is different than the word that is used in the Quran to describe creation of for example, the universe and the Earth. The word used to describe the creation of the universe and the Earth is more like creation ex nihilo. But the word used here means more like "turning something into something else". This verse obviously cannot literally mean that living things are made from water because this is untrue. Instead the correct interpretation is that water is a prerequisite for life as we know it. After a planet, stable atmosphere, and good temperature, the most important thing needed is water. We know that life on Earth started in the oceans. Specifically, the oceans contained the amino acids and minerals along with water needed for life and God "turned" that into a living thing. And when we search on other worlds for life, after determining if they fit in the habitable zone around their star, what is the *first* thing scientists try to search for? It's the presence of liquid water. It's that important to life. That's what this verse points to.