Existing Valleys incorrectly installed

"I recently purchased a cabin in the White Mountains with a metal roof. During the inspection the inspector pointed out that the valleys on a portion of the roof were installed incorrectly. I have attached a satellite photo that shows the roof. The red section is my problem section. The valleys on both sides were installed under the green roofing but on top of the red roofing (it looks like the red was installed first). It looks terrible with the valley flange metal bent up and down over the ridges of the red panels with what looks like RTV sealant everywhere. If you look close you can see 4 skylights in the red section. These were also incorrectly installed and there is water staining around them. My question is this. I know I am going to have to fix the flashing and maybe put a cricket on the skylights. And I know I should fix the valleys. But do I tear the whole section out or try to fix it, replacing the valleys and select panels? It just seems like such a waste to throw out good panels, even though they are red. I will try to post more pictures (I have some that the inspector took)."

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