Contractor Only Replace Half of Roof - Options?

[Tim Porsche]

Hi All,

I have a bit of a situation here and would greatly appreciate any advice on how to proceed. I purchased a rental property back in Spring of this year and decided to replace the roof on it because it's quite obvious it has reached the end of its useful life. The roof can be divided into four main sections.

1. The main section of the roof. This is about a 600 Sq. ft area and is a flat roof.

2. The front porch roof. Relatively small section that is rubber.

3. Back area of house roof. This is about a 150 sq. ft area that covers the back of the house where the kitchen is. Also a rubber roof.

4. Back porch roof. Very small section that covers the back porch. Maybe 50 sq. ft.

The contractor replaced the main section, but nothing else, and is claiming that is all he bid on. He also charged me extra to remove two extra layers of roofing underneath. Now, when I originally contacted the roofing contractor to get a quote to replace the roof back in June, I never differentiated between any of these sections. When I told him I wanted "the roof" to be replaced I assumed he realized I meant the WHOLE roof, not just the main section. I had never thought a contractor would replace only certain sections of the roof when you tell them you want "the roof" replaced. Looking back this was a mistake on my part, and in the future I'll make sure to have as much detail as possible listed in the contract about EXACTLY what is included in the price and what is not. 

The only written proof I have that I wanted all sections replaced is an email where I stated the following to the contractor's assistant, and also the contractor himself who was copied on the email:

"Hi Name,

Thanks for the quote, I appreciate it! A couple of quick questions for you on the roofing product used though. Will .060 TPO be used on both the flat portion of the roof and the slanted portion and porch roofs, or just the flat section of the roof? Also what is the average life expectancy of .060 TPO roofing for flat roofs? I'm not familiar with the product so I have no idea.

Thanks!"

The contract itself states the following:

"Specifications: Proposed Cost

Roof

Remove & dispose of the existing roof, if additional layers are found they will be removed at $50.00/sq.

Inspect current roof deck, if replacement is needed it will be completed at $1.65/s.f.

Install 1⁄2” fiber board to the entire roof deck using screws and plates

Install .060 TPO to the roof with all needed flashings and trims

Install perimeter metal with all needed flashings

Proposed Cost: $3,300"

I guess my question is, what options do I have at this point? Do I just suck it up, pay, and then get someone else to finish the other sections of the roof? I know I made a mistaken not specifying exactly what needed done in more detail...but honestly, when you say you want the roof of a house replaced, wouldn't most people assume you mean the whole roof and not half of it? 

Thanks in advance for any advice.