3" ain't too bad Mo. The trick is to see if there is any horizontal or vertical cracks above where the edge of the flashing up behind the cedar is. And vertical joints as well.
If you can see in any crack or joint, and see the top edge of that flashing. The water can see it too and get in above the top edge of the flashing. Usually on a certain driving rain that would pound against the cedar & flashing. But if it looks tight, 3" should be sufficient. I am wondering how you saw the flashing guestimate the 3".
If you were seeing it through a crack or joint, then water driven rain will find it also.
The urethane caulk does an excellent job of sealing. Lasts a long time also. I would still suggest a drip edge flashing up a couple 2-3" under the roof edge, then bent down over the window tops with a 1/2" kick out or "drip edge" to be specific. But tis hard to tell all from pictures, well not as easy as seeing it in person. If its tight along where the window meets the siding. You'll be ok for a while at least. But it should have had a drip edge flashing under the cedar & over the window edge to seal it off. Then caulk would not have been needed.
After looking at the full picture, I really don't see alot of water getting to that small bay roof. If you can make sure the top of the bay roof meets the siding is tight, and the lower edge over the windows is tight. you should be golden then. That roof just will not see enough water to cause a major floodstorm in those windows.
Pretty much same goes as missing flashing at bottom of other window. Where u cut & replaced siding & caulked. Will most likely be trouble free for some time hopefully now. But windows should have a base flashing at the bottom that the window actually sits on, with the same type drop down & drip edge. Same at the top with a pc of header flashing. At this point that may or may not be involved. I have snuck pcs of flashing over or under windows before. But a few tight spots make for a miserable day.
Just be careful NOT to caulk natural drainage paths built into the window system(s). Yes I was not overly concerned with the modular channels, as they run vertical and are made to drain naturally. The channels are basically outside the house or room. Almost all windows, doors, sliders etc, have drainage provisions. You want to make sure to keep these clear & clean.
Agway sells a really good granular product to kill ants etc. Just a pour a lil in when putting your wood back in then forget about it. Might even be the stuff you mentioned. My mom uses it and swears by it.
It seems to me you have the leaky drain & these windows back under control and performing as expected. If ya want, get your hose out and douse the top of the bay window roof, the siding where the flashing from the bay roof meets it. anywhere you feel might have been a leak path or problem. I do however suggest starting at the lowest point and spraying your way up. checking periodically at each height advancement. If you test with water at the top first, it could come in there and drain lower, giving you some guesswork as to where it originated from. Starting low and checking as you go up. You will know exactly at what height or level the water is coming in, if it ia at all. Still sounds like you solved 2 major PITA problems. Thats a great feeling, I know, I am on red alert every other day here" Oh Mr. fixit man". But it feels great when a problem is fixed and you can breath a sigh of relief along with feeling some pride in a job well done. I just hate fixing builders or previous homeowners F-ups. But we all do, and you will with any house.
If ya have any other questions you have a couple folks here that can try and give answers. Let us know the next project, so we can help prepare for the remedies if able
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!! Your correct. Most think water will just run down & drip or fall off. But it will follow the lines of the object it is running down.
