Trouble

Tks tinner but I dont think u get the pic. Window is not a problem at all. Have you ever seen a situation like this where the stone dissapears half way up the roof? I doubt it. I have not and I dont see any way to waterproof with a guarantee. It may have worked if they had framed an offset so the back half of the wall, with shingles on it, would be even with the 6 " stone

Something like this might make it easier for you.

That doesn't look too complicated to me. Ask the carpenters to drop that window at least a foot to give you at least a little challenge.

Use a larger than normal tinner's wing on the corner and I'd make the steps 8-10" wide assuming th erock go to the deck. Were the carpenters smart enough to slope it away from the wall like a cricket to help guide water from the wall? If not, I'd put a flat piece of 6" I&W at the wall, followed by a 12", an 18", and even a 24" piece. Then, if you want, run a 36" to and up the wall. Then add something under your through flashing to go over it AND your flashing. This is SBS, but the theory is the same. The water runs away from the wall. Every little bit helps.