The LBS has nothing to do with the warranty other than being a middle man between the manufacture an you.

For the different frame supplied, was the bike model you had back in 2007 still made in 2014? (you don't expect them to keep frame back from 2007 just in case they need warranty swaps) If it is still made, is the frame the same material? If it is made, is the frame used over multiple different models, so this is just a decaling issue? have you asked your LBS the difference between the frame models in the range?

Guessing from the model of the bike you mention, you have a Trek? Whatever frame you got, a 2012 frame will be stronger than a 2007 frame, as there are different standard used now, to then, specifically CEN, it's a EU standard, but all bikes coming from TW/CN will be built to it, this was introduced in 2010, so your new frame will be stronger than you old one,

For the amount of time take, 6-8 weeks isn't that bad, have heard and experience longer for bike parts to be replaced under warranty, if you want updates, could you not have contacted the LBS, and asked them to contact the manufacture on your behalf?

Would be interested in why the need to change the rear brake, the spec for the brake (post) mounting has not changed in the last 15 years or so, so there should be no need to change brakes, the headset would have changed from EC to either ZS or IS, so that is understandable.