Contractor #2 came and went and I must say that he spent a lot more time looking at the job and asking questions. Unfortunately, he also bases furnace size on square footage, though he did agree to take a sheet of data (dimensions, wall and ceiling construction) about my house back to the office and do a calculation.
Who ever put in the AC created a bumped out area on the furnace plenum to get the A coil in and he said the A coil needs to be reoriented to be correct. So that adds a little to the price, though he is also quoting a Lennox vs an Amana.
I think I'm convinced that I want to go with a two stage burner with a variable speed motor.
I appreciate the feedback from all of you.