Where in Nor Cal are you - Coastal, Bay Area, or Inland (unlikely if summer max is 91) ?

Inland (Santa Rosa) and you are right it gets hotter than that in Aug

I'm in your general area but to the south. How old is the house, how well insulated and how tight? (But I'm a fellow homeowner, not in the business, but have had major HVAC work done in the past 2 years)

House is 60 years old... 2x4 walls and new insulation to R-11, attic at r-30 and floors to R-19. House is tighter after air sealing-- went from 12 ACH50 down to 4.

I should preface my comments by saying that while I consider myself to be practical, I'm not an engineer or a person who is militant or uber-motivated about building science. I like to do what is practical without going to the n-th degree with what may be possible (and ecologically sound) but not economical. We've beefed up our attic to a bit more than R-30 but took the advice of the insulation contractor who said insulating the floor was probably not worth doing. We have put in double windows throughout.

I have a house about the same size as yours. My enlightened HVAC contractor had originally proposed 6 tons of cooling but agreed that 5 tons would probably do fine. It has been fine, long runs and very comfortable on the hottest days.

With that in mind, I'd be concerned that 3.5 tons may be a shade small. 3.5 tons is 42000 btuh and since your load calc is at 44K, I might round up the small amount to 4 tons (48K) rather than down. It's a small difference but I'd rather be off slightly (and only slightly) on the high side than on the low side.

You've cited a modulating furnace and that should provide good comfort. One concern, and a reason why I avoided a variable speed unit, was the thought that the fan operating at a low speed might not push much air to the far end of the ducts. My contractor agreed with that as a concern and so we didn't go that route. My house is > 100 feet long.

If your HVAC contractor says that the max performance would come from a thermostat of the same brand (ie, Bryant), I would go with that. All up-market units have internet accessibility, you should be most concerned with its function.

HRVs? I think these aren't common in our area except for the newest and tightest houses. Mine's about 50 years old and I like a small crack in a few windows, and sometimes with a bathroom exhaust fan running, to bring in fresh air.

Good luck, take my comments as just one guy's personal opinions.

PS - I too have Bryant equipment and am about to buy more for a second house. I'm very happy with it. But more important is having a great contractor. Good equipment doesn't make up for a crappy contractor.