We recently bid on supervising a partially completed roofing job for a resort on the coast of Oregon. During the bidding process, we offered the property owner some free advice about nailing, protrusions, pipe jacks, rake edges, and starting roof jobs late in the season when they might encounter rough Oregon coastal weather.
Probably the most crucial aspect. So far this year, I have had two brand new roofs torn off because of very bad nailing. If you hear the roofers going super-rapid-fire with the nail guns, that is a big red flag. ALL nails must be perpendicular to the deck and flush with the surface of the shingles. Use six nails per shingle and use stainless steel nails. Sides of roof facing ocean should also be hand sealed. Nails must be placed at certain points, not just anywhere. Nails that are tilted, raised, or pushed in too far are not acceptable and could void the blowoff portion of your factory material warranty.
All roof protrusions should be double sealed, meaning that sealant should be used both between the top of the shingles and the bottom of all fixtures/protrusions as well as the shingles that cover the tops of all fixtures/protrusions.
I hope they are using two piece lead plumbing pipe jacks and not the rubber/NCF "no-caulk" jacks. And, they should be using continuous ridge vent or copper attic vents; no steel vents as they will soon rust. Plastic vents most economical approach but keep in mind that the plastic vents will fail and need replacing before the shingles do.
Rake edges (if any) should have a bleeder strip that is sealed between the gable/rake edge flashing and the underneath side of the bleeder strip. Shingles and bleeder strip should extend a good quarter inch past the edge of the rake metal.
Weather in Coastal Oregon:
We have been blessed with this dry run weather wise, but it will end soon and what is in store for us at the end of that rainbow? When the weather goes south, it may REALLY go south. You may want to consider stopping the roof work at a certain point and finish next year. It will soon get to the point that for each step forward, you may very well take two steps backward and expose yourself to weather related 'issues'. Your roofing company should have manned the job with more guys; but then again, they would have if they could have. I know how these guys think. I am kind of surprised that such a large project was started so late in the year.