Cw

I don't like that sizing at all for heating and cooling.

Basement finished areas at or partially below grade normally have low heating and cooling loads depending on insulation properties.

Heating a main floor beneath a second floor is not as great either. Of course, you have vaulted ceilings in one area of the main floor.

I agree a two ton is probably too small but the idea of a 4 ton seems oversized.

Back up and thoroughly review carefully before making a decision.

IMO

Thanks for your input but I wanted to clarify a bit more. The figures from their load assessment indicated:
96920 Btu Heating
44010 Btu Cooling

Based on that, the suggested 4 ton unit makes sense doesn't it? I mean there isn't a 3.5 ton unit so if a 3 ton AC is 36,000 Btu then it would be 8,000 Btu short and the 4 ton at 48,000 Btu would be the only choice although 4,000 Btu overkill.
Also, they mention "Balancing dampers will be added to all supply ducts at the supply plenum" which nobody else did. I am just reluctant to write them off if they really have their act together and the proposal has merit. Unfortunately, this is a hard decision for me to make without more experience and technical knowledge. By the way, both of the contractors that did the load assessments are Trane "Comfort Specialists". Does that have any real value or just a marketing gimmick?
Again, thanks for any input.