We just went through a total redo of our furnace (was oil, changed to gas) and AC system). We already had ducts etc so less of a big job than you have---ie, needing to put in a brand new AC system. We also had an existing gas line into the house, which if you have, will make the changeover much simpler. Anyway, we used William Day out of Delaware ###-###-####). Also had a bid from Oliver, which is larger and more well known but we found them far more expensive and Bill Day was more knowledgable and well priced. Bill is an exclusive Carrier re-seller, which was important to us because we had researched them extensively already and knew we wanted to use Carrier products. Another thing we got from Bill was a really informative analysis the day he came to see our home, showing cost differences between using oil and gas. We actually didn't know if it was best to switch from one to the other. This analysis was extremely helpful and he was the only contractor with the computer programming (with him) to do so. So it's been 2 months I guess since we got the new systems in and they're awesome (never knew I'd be so happy with new AC)--but our our 30 year old system just didn't compare. We went with top of the line for maximum energy savings and benefited from a Carrier rebate. We also had a small bit of ductwork done to increase airflow into my office, which is quite warm due to sun and computers running.
I know this is big decision for you, but having just been through it (and having been actually happy with the contractor---and the guys who came to work in my home), I felt compelled to reply to you. This is the first time I've had this experience with a contractor---we had our kitchen totally re-done a few years ago (not so pleasant!) so wanted to pass on a good name in the business.
Good luck!!