Couple questions

First, this

I don’t think this picture does it justice, but this roof is like rolling hills. And not up the roof like crowned rafters, but across the roof. Sometimes 2 and 3 feet apart, somtimes more. It is a 1x deck. 1 layer of shingles as far as I can tell. Has anyone ever seen this or know whats causing it?

Also, any advice on how to flash this chimney?

I am thinking some really really really tall counter flashing.

No idea about the ‘rolling’.
I wish they’d outlaw those pipe collars. WHen they give out, water just rushes in.
Chimney can be done normally. I’d run the pan all the way across with only 2" tinner’s wing. Wall side of the pan would blend in with the step flashings like an over sized one. No trouble there.
The couner=flshing could be tall if nothing else works.

How thick is roof deck and what kinda venting??

Could it be loose 1X that the shingle’s are pulling up? I suppose you wouldn’t be asking if that was the case and you were already up there.

The chimney… I would go tall like you said or go small and make it a one piece. Just bend it the front and back wrap so it will stay on its own. Pull it off and caulk it in place, nail the front wrap and the back wrap. Try the small first.