Roof leak from inside.  So this what the customer noticed and called GAF about.  GAF notified Litespeed Construction that there was a roof leak on a Golden Pledge Warranty, and the contractor who had performed the work is now out of business.  Litespeed came out to look at this problem for GAF.

The Chimney cap is the reason for this roof leak. Not the shingles or flashing. Proposed a new metal chimney cap.

The nail pops are a huge risk and issue for warranties.

Roof deck boards are not rotten here, they are just a little soft.  This probably is not an issue for the roof integrity.