Never done this (posted to discussion board) before but need some guidance. Had a new roof installed (in coastal southern California - no snow) (GAF Timberline High Definition shingles) and the contract specified, For low slop sections, “torch apply granulated modified membrane with 3” side and 6" end laps to the  field areas. . ." For the more normally pitched areas, “Install a double lap layer of “GAF” Tiger Paw synthetic underlayment to the roofing surface using large head galvanized roofing nails to ensure proper placement.”
It was discovered during the roofing process that only a single layer of underlayment was installed on three sides (fields?) of the garage roof and part (one field?) of the roof over the house. Contractor acknowledged mistake, apologized and asked what he needed to do to make it right. Said he’d rip off and redo the garage areas if I wanted (but he’d rather not) and offered to kick back some $ for the error. Didn’t offer to redo the area over the house that only has single layer.
Also, when I arrived on day three, I was told that they weren’t installing the proposed granulated modified membrane, but were using a better product - don’t know what it was or how many layers were put down, but it was applied using a torch method. Will ask today.
The signed proposal/contract includes a “GAF” System Plus Warranty.
My concerns are, (1) the System Plus Warranty doesn’t cover workmanship defects which it seems is exactly what I have. The manufacturer offers a Golden Pledge Warranty that does cover Workmanship Coverage for 25 years. I’m thinking this is what I should ask for to cover myself (in order to make things right), and (2) I puzzled why the foreman unilaterally changed the product he applied to the low-sloped section of my roof, and I honestly don’t know if he did me a favor or not.
Lastly, the job will be done later today. I still owe 50% of job price. I think the contractor and I need an additional day or two to sort all this out. Should I hold back the entire 50% until we reach an agreement, or pay some portion and hold back a smaller percentage? Just want to protect my investment and I’m feeling like an amatuer in over her head. Any advice would be very much appreciated. Thx!