My job has about 21 square of shingles and also a flat rubber roof on a porch. 

You have a few different materials used in that foundation, i agree with @Russell Brazil on this, yes there seems to be some " handyman" work done, but nothing bad enough that can not be fixed with some jacking up and repairing certain areas. the contractor probably does not want to bother with it ( who knows, he may want the property himself after seeing it) so he is trying to make you think there is a ton of work to either give you a high price or hopes you will walk away so he can grab it. the roof, plan on installing a new roof, shingles look close to their life span and not because of the color, look at the gaps between each tab ( the views from above show it best) when they start to widen up that means the shingle is drying up and close to the end of it's useful life.

The roof is 10 years old shingle.

If so, were permits pulled & were they installed by a professionalAre any of the homes rented to studentsIs there a flat roofare there asbestos shingles The Year that the following were updated (either partially or fully) would be good to know:- Heating systems- Roof- Plumbing- electricalSome companies will not write properties with systems that have not been updated.As long as you are living there, the proper policy for a 1-4 family is a "Homeowners" policy.

If you are not familiar with roofing you can easily be taken advantage of...15 yr shingles, no underlay, no ice guard, old shingles not removed, chip board sheathing material etc. 

Are they low-grade shingles or better quality architectural shingles?

The shingles look like they are in good condition, but the flashing and the gutters definitely need some work.  

Asphalt shingle roof for a house that size is about $6,000.

The house presently has 2 layers of shingles and there is a leak over the bathroom.

.#3 Contact Local Contractors for PricingCall local Subcontractors and get budget pricing for common repairs on your typical rehab project.For example, call a roofer and ask what their average cost per Square of Architectural Asphalt Shingle Roofing would be on a 1,500 sf house, with a 6/12 pitch.Note: Some contractors will be reluctant to share pricing without seeing the property, but tell them you are just looking for a rough budget number you can use on future projects.#4 Compile Your Prices into a Spreadsheet or Estimating SoftwareOnce you start to get a better understanding of Labor and Material costs you will want to store this data into a spreadsheet or software that you can use to help you streamline the estimating process.The Book on Estimating Rehab Costs comes with a spreadsheet that you can use to help you populate your own database of labor pricing and material pricing.