I assume the GAF quote was for Timberline HD as opposed to Timberline Natural Shadow which is a lower quality shingle. If this is the case, the shingles are all comparable. The iko warranty is actually longer for the initial 100 percent coverage period, 15 years as opposed to 10 years for the GAF and certainteed.
Prices vary widely from contractor to contractor as does the quality of work. Quality often is not reflected by price, meaning the higher bid is not always given by a higher quality contractor.
How big a percentage of the quoted prices is the $2000? Are the contractors all including the same ventilation and flashings? Is soffit ventilation adequate? Is price for potential decking replacement speced in the quotes? Are contractors insured? Make sure you are comparing apples to apples. I'd definitely talk to the other people in your area who have had their roof done by the IKO guy to make sure they would recommend him. Also, if you decided you want to use a specific product, any installer worth his salt should be able to install any of these products.
I live and work in mid Michigan, and I'm guessing our climate is similar to yours. We install ice and water shield to a point 2' past the interior of all heated walls per code and to all valleys. Synthetic felt or standard 15#/30# felt to the remainder of the roof deck.
Good luck! And get references