Roof leak problem

[Dusty Britches]

We built our house 11 years ago and recently discovered a leak from a pipe jack through the roof.

We have a Mueller Metal roof that was installed by a sub contractor. Upon discovering the leak, we contacted the insurance company, got an adjuster out who said within minutes that the roof was not properly installed around the pipe jacks (see pics below). The photos were taken with my friend's drone. While we can caulk it, we have a bigger problem with the improper installation. (In case you need help seeing it - the roof should overlap the high side of the pipe jack.)

Fortunately, it was properly installed around the chimney. (last photo)

I noticed this almost right of the bat when it was built but I thought the contractor knew what he was doing and everything would be ok, but in the back of my mind I was worried the day was coming that we would find leaks. I have 5 pipe jacks that need to be addressed.

I'm not sure how to proceed with this or who to call. This is obviously not a job I want to even think about fixing myself. I'm looking for plausible solutions.