Hi Chuck,
Boy, you have places that just want to leak everywhere.
The majority of it needs to replaced, I would tear it all off. Unfortunately that's costly. The first layer is one price the second is another. That means 70sq of roofing to be removed. If they want to get picky they can add on more for two story and then more for the areas that are 7/12 to 8/12.
The most important thing of your whole job is proper flashing. Anywhere the roof meets the house it needs to be flashed and flashed right or it will leak. The best flashing known to man is copper. It isn't necessary. The next best thing is aluminum. Do not let then use galvanized. It will break down.
Your porch needs to be re decked. Depending on the spacing of the rafters. If it's 16 on center you can use 5/8, if it's 24 on center you need 3/4. I would probably use 3/4 regardless. It very important that the flashing is up under the siding. If there is a pitch to that roof, ( I can't tell from the photo ) you can use water and ice. It's a form of a rubber membrane.Then put regular shingles over that. If it's completely flat, It needs straight up rubber.
The top part of the roof, that looks to be 3/12 I would put water & ice at least six ft up. It looks like snow would just sit there. And down the rake three ft. in.
Three ft. in and across the bottom on the rest that's 7/12 to 8/12.
The chimney, if they tuck point it make sure they do the cap on the top too. It needs to be stepped flashed then counter flashed ( with aluminum that matches your roofing ). If they do it right the counter flashing needs to be two inches higher than before. They'll chalk a line and grind into the brick and put new flashing in. It will never leak again in your lifetime.
All the soil pipes need to be sanded and painted before the new roof goes back on.
As far as price... I don't really know the labor cost there, maybe things are higher. The big company's always charge for p/o, profit and overhead. I wouldn't say no to the little guy, he might do a better job. The bigger company's use the people that are not responsible enough to work on their own. Not alway's, but you get my point. Ask a lot of questions and find out exactly what your getting for your money. Then watch them as their doing the work.
I think I've covered everything.
PS. Make sure and keep your gutters clean, if you don't thing can't drain.