Hello All -
I could really use your help if you have any input for me.
I live in Austin, Texas, in a 3600 sq foot (of which 1600 sq feet is upstairs) home that was built in 2005. My home has a vast open area that connects upstairs and downstairs. There are 4 rooms upstairs.

No one can tell for sure (the name plates have faded in the sun), but my downstairs is probably a 3.5 ton AC unit and my upstairs unit is a 2 ton unit. Both are builder model Carrier units.

The non-carrier brand coils on my 2 ton AC unit are leaking. Rather than dump ~$1800 into fixing the coils, we would like to upgrade the size of the unit. good luck getting any AC company to perform a manual J calculation. I mean, I called out two reputable companies (nearly all 5 star reviews on Yelp and positive reviews on Angie's list) and they weren't interested in performing a manual J calc. But everyone agreed that the upstairs AC was undersize - and I agree. During the summers, it will not keep up with the cooling, it runs all day but still the temperature upstairs rises.
I finally hired a home efficiency company who said that my upstairs needs a 2.7 ton AC unit (based on their Manual J calc).

I have quotes from two different AC companies.
Company number one:
Quote A ($4800):
Trane XB13 Series 13 SEER 2.5 Ton R-410a - (Puron) Full Straight AC System with Matching - Trane 2.5 Ton XB80 Gas Furnace
Price includes equipment, labor, code upgrades, taxes, and warranty.
Price includes adding return ducts to each of the two bedrooms beside pull down ladder.

Quote B ($6900):
Trane XR17 Series Two Stage 16 SEER 3 Ton R-410a (Puron) Full Straight AC System with Matching Trane 3 Ton XV80 Variable Speed Gas Furnace

Company #2:
Quote C:
Comfort 16 SEER with Variable Speed Furnace, single speed compressor
8176.00
(1500.00) Internet coupon discount
6676.00 credit card price
**6258.00 cash price**

Quote D:
Performance 17 SEER (24ABC636A-3) with Variable Speed Furnace (58CVA070-1-12), 2 stage compressor
9594.00
(1500.00) Internet coupon discount
8094.00 credit card price
**7588.00 cash price**

Quote E:
Infinity 17 SEER with Variable Speed furnace, 2 stage compressor
10402.00
(1500.00) Internet coupon discount
8902.00 credit card price
**8346.00 cash price**

I think that I like the idea of a variable speed furnace. We can afford a two stage AC unit. Right now because my kids are off at school or other activities during the day, I program my Nest thermostat to allow the upstairs to get hot (82 degrees) and then start to cool down before nap. Then get hot again, and cool down before bedtime. Company 2 AC guy said that with such big swings in temperatures, that a two stage unit would mostly be running as a single stage, and not to spend the money on a dual stage if I am going to program my Nest that way. Company 1 AC guy said it uses more energy to program the way I was doing it, and to only allow it to raise a degree or two during the day so that it does not have to work so hard to cool back down. In this case we would see more of a benefit from a 2 stage unit.

I don't know what to do. and then there is the whole trane vs Carrier thing. Does anyone have any advice for me?
thanks SO MUCH for your time.