I didn’t do anything except number 4 and 5 (I left the excess garbage on the curb in plastic garbage bags) and for the light switch.

I literally told them I did not need it or want it but the system requires it based on a surgery I had, even though I am 100% capable of working.

The surgeon doesn't do surgeries on his first day of medical school.So be careful!  

Just purchse one of the back pack plastic garden sprayers and really soak the roof.I am assuming firbrglass/asphalt shingles not wood shingles.There is also a zinc product that works well and if you are installing a new roof you can purchase zinc strips that are installed beneath the cap shingles with a small 1/2 inch band showing it will keep the black stains from starting.

How many trauma surgeons watched videos, read a book, and then jumped right into surgery.

Son lives in the Inland Empire and asked if I would be willing to go to the house prior to meeting him and cover the roof with plastic.

DAP also makes a clear elastromeric sealant that is available at the big boxes which can be used  in a pinch.....we just prefer the other.Don't let roofers use plastic boots....you have to check them on this....use the aluminum based boots for a longer solution and run a bead of sealant around the upper edge of the rubber grommet that seals against the vent pipe.  

That is a mistake and you can read many of the horror stories right here on BP from newbie's who failed to understand that if they won't read a medical book and perform surgery on themselves, it's probably not a good idea to read some blogs and start drafting contracts with no knowledge of the provisions and consequences of such an action.

In fact, I'd rather have the original windows than new plastic ones.

The plastic connections, along with copper crimp rings, are cheap and easy to use.