The blower motor in our upstairs HVAC system just burned out after 26 years. Our first thought was simply to replace it, but enough alternatives have since presented themselves that we could now use a little help. Salient details:

HOUSE

Location: US West Coast, latitude 37.4 N (Page Mill exit off I-280)
Finished basement: 900 sq ft
Downstairs: 2600 sq ft
Upstairs: 1000 sq ft (MBR, MBA, 2 walk-in closets, hall, study; the study is the only upstairs room occupied during the day)
One staircase connecting all three floors.
Windows:
....many large on east and south sides
....typical size on north and west sides
....all double glazed
Skylights:
....12 downstairs
....6 upstairs

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HVAC
Basement furnace heats basement and downstairs, so serving 3500 sq ft
Upstairs furnace+AC heats/cools upstairs, so serving 1000 sq ft
Summer: upstairs and downstairs are kept cool by upstairs AC.
Winter: downstairs and upstairs are kept warm by both furnaces.

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ELECTRICITY & GAS

PG&E + 7.5 KW roof-mounted solar PV

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CURRENT SITUATION
Upstairs blower motor burned out.
Could replace motor.
But upstairs AC is 1988 Carrier---inefficient, and lately ineffective.
Time to modernize upstairs furnace+AC.

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PROPOSAL 1:

Cond: Trane XR-14 3-ton 14-SEER Model # 4TTR036
Evap: "matching"
Heat:
(i) Trane XL-80 2-stage 80kBtu @ 80% AFUE (= 64kBtu); or...
(ii) Trane XV-80 2-stage variable ditto

PROPOSAL 2:

Cond: Bryant 3-ton 16-SEER Model # 116BNA036000
Evap: ADP Model # C36A142C126
Heat: Bryant 1-stage 70kBtu @ 80% AFUE Model # 311AAV036070
(Contractor quoted only a 1-stage furnace on the ground that a 2-stage furnace wouldn't fit in our narrow furnace closet.)

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OUR USE CASE:

Heating: Very light use of upstairs furnace: only in winter, and just for an hour when we get up in the morning. Even with the furnace currently on the fritz, the upstairs study is kept warm enough during the day by the combination of sun, downstairs furnace, and sweater (rarely needed). The bathroom however could use a little blast of heat when we get up.

Cooling:
....Intensive use from spring to fall.
....Made more intensive by downstairs being cooled from upstairs.

(So: little to no cost benefit from an efficient upstairs furnace;
but much larger cost benefit from an efficient upstairs AC.)

Quality: Preferably higher (not trying to cut corners)

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QUESTIONS

Assuming this HVAC system lasts 20 years (we got 27 years out of the two Carrier units) and is used much more for cooling than heating:

1. Any significant reduction in energy consumed over 20 years if we go with the variable-speed Trane XV-80 instead of the XL-80?

2. Any reason why a variable-speed Bryant furnace would require more closet space than a 1-stage one?

3. (Blast from the past.) We have an MIT-designed 1988 Unity Home Manager thermostat system with 12 zones (that it controls using dampers in the ducts) that continues (amazingly) to work fine. However it can only act as a one-stage thermostat for each furnace. If efficient cooling upstairs is our only concern, will this one-stage thermostat suffice for a variable-speed blower motor, or will we need to control it from a different thermostat? (If the latter, presumably any such thermostat will have no idea how to operate the dampers, so they'll just have to be left 100% open with the whole upstairs operated as a single zone instead of the present four.)

4. (Wishful thinking.) Any Unity Home Manager hackers in the SF bay area?