Does my house have the wrong roof?

Future-Proof: Navigate Threats, Seize Opportunities at ICNY 2018 | Jan 22-26 at the Marriott Marquis, Times Square, New York

Q: In 1988, we had a new roof installed with 40-year limited warranty fiberglass shingles put over our gravel roof. While the roofers were working, dry rot was discovered in the kitchen, and we had it repaired. Since 1997, there has been a widening area on the ceiling (where the dry rot was repaired) showing yellowing and the start of crumbling plaster. We were told by the contractor who repaired the dry rot that the yellowing was salts leaching out of the plaster. We contacted the roofer and were advised to caulk around the outside of the building where wind might be blowing in moisture. In January 2007, the roofer said the yellow color of the plaster means water is present. I also noticed the wallpaper bubbling near our fireplace. The roofer said the nails holding the shingles had rusted through because of fog and dampness and water pooling to low places on the roof. He recommended a new roof and would use copper nails and what he said was an "Alaskan" shingle ...