Oh boy! My 2cents probably wont help much cause i usually tear off stuff like that. I can say though that i tried to repair some copper shingles similar to those and wasnt able to. I ended up having to take them off and once i did, the foot traffic over the years smashed up the locks on the seams and we couldnt get them to go back together in a way that made us feel comfortable so we replaced them. I was surprised, thought i could do some surgery for sure. Not to say those shingles you dealing with are the same though.
I dont like the flashing detail and not sure it could be done much better. Some of these products are designed in a way that limits our detail options. For the skylights, i would yuck them all out, raise them all up as one enough to get a cricket behind them then close it all in as one. That would take a lot of time and money though. If the budget called for repair on this one id get a couple cases of vulkem.