Two story Colonial just north of New York City requires complete replacement of HVAC equipment. It's my dad's house, and I do not live local.

Current equipment installed in 1991
-Lennox G20Q3E-125-1 125,000 btu 80% furnace
-Lennox HS22-411V 3-ton condenser
-Lennox 3.5-ton cooling coil

House constructed 1968
-Wiring and pad placement indicate cooling added later
-Motorized dampered zones for first and second floor heating. Cooling single zone.
-First floor fed from basement. Basement partially finished after construction, with two registers connected to first floor zone.
-Second floor fed from exposed attic, trunk from basement rising in center of structure. Attic ducts moderately insulated. Rooms have high registers and low returns.
-Low wall returns in entry and second floor halls

Heating comfort is acceptable, but system quickly cycles except on coldest days. Cooling on second floor has always been barely acceptable, with first floor and basement very cold. Must close supply registers in second floor bathrooms and hallway to cool bedrooms.

Heating and cooling loads completed in 1991 using Logic 1000 Residential Loads Analysis software
-Heat 57,620
-Cool 34,161
-1820 sq. ft.
-Manual J7
-Winter Inside 70/Outside 0
-Summer Inside 70/Outside 90
-Basement not included in calculations
-I believe one north facing wall was accidentally not included in the calculation

Heating and cooling loads completed using HeadCAD 2014, based upon 1991 data. Also includes missing wall from 1991 report, window/door changes since 1991, and basement.
-Heat 62,748
-Cooling 34,598
-2413 sq. ft.
-Manual J8
-Winter Inside 70/Outside 12
-Summer Inside 72/Outside 87

For the life of me, I can't figure out why the contractor in 1991 installed such a large capacity furnace when he had such good data from his load report. I believe he was replacing an A/S 125k unit. He was an old school heating guy, for whom I have much respect.

Here are the proposals received so far. Of course, no contractor did an independent load analysis. We shared the 1991 report with all bidders. I did the HeatCAD 2014 report.

Contractor 1 - old school guy, says ducts oversized, thus requiring 5-ton blower for adequate cooling.
Trane TUD2C100A9V5VB
Trane 4TTR3042D100A
Trane 4TXcc043BC3HCB

Contractor 2 - did not provide specific model numbers or coil info
Lennox ML180-110
Lennox XC-13-042

Contractor 3 -
Trane TUD1B080A9361A
Trane 4TTR6036A1000A
Trane 4TXAB031BC3HUB

I'm looking for advice, suggestions and guidance as we go through the bidding and solution selection process. Getting my dad to take action is relatively difficult these days. Making his life simple and easy is my best strategy.

Thank you.