I know South Bay is a bit more moderate than say Walnut Creek, and my house is 94 instead of 97 and only about 1750 sqft volume / 1450 sqft space, but I think based on my observation I can give you a bit of an opinion of your manual J calculation:
1) My typical max temp outdoor is up to 84F, worst case 91F, and my 3 ton is running 50% if my outdoor temp is 80F and I set my thermostat to 76F. If you think your house in Walnut Creek will suffice with 3.5ton you are going to be expecting it to "sometimes" not cooling to the precision you set it to, and you may have to settle for it being a few deg higher because you are cutting it too close. It is good for efficiency most of the time, it may be exactly what you want if you are using both a minisplit and a central in the worst case. 3 ton for sure is too small for you and you will need at least 3.5 ton, and I would probably do 4 ton if I don't have duct issue. Oh, I have a north facing roof, and if you have a south facing one expect to use more AC than that too.
2) You probably won't have 27F all winter, I don't think that's how cold Walnut Creek usually get to. In South Bay I am seeing 45F in the winter sometimes but usually 50F, I think you are probably ok with 60k BTU, even if it means you may have to turn on a few computer to supplement the warming in the winter. At night when you sleep, assuming you are upstair, you should be "warmer" if you are undersized.
3) You mentioned you don't want to have a mini-split as supplement, but this may actually be allowing you downsize your central to 3 ton and you can add a 1.5-2 ton mini-split or even window unit upstair to supplement the overall system. Sure it looks ugly but this is probably the most energy efficient way to make the system perfect in size, and if you use window unit as a supplement, you don't even need to worry about multi stage furnace, AC, duct size, and you can just go with 3 ton 60k BTU and call it a day, and only turn on the window unit on those 90F days, with not much labor cost.
My other opinions:
1) Back in the 26c/kwh days I know people yanking out heat pump for gas furnace because kwh is 5x more expensive than therm for the same energy. Even if heat pump is 2x as efficient it won't matter, you are using way more than you will save.
2) 80% furnace here all the way, unless your house is build with 90+ you will spend a lot on the flue work remodeling and you will have to deal with a lot of cost venting them sideway, condensation, leak, etc. Not worth it if you are paying someone to do it (labor is the biggest cost you will never get back ever). Since it is a 97 house, it is not build with 90+, it is not worth it.
3) Buy something that you can buy parts and replace if things go wrong. I don't like having to call someone for a service just to get parts (York? Lennox?) but someone I can buy parts off internet and install myself would be better. Parts are cheap, even if you are paying $500 every 5 years for something stupid, but each tech visit out of warranty would cost you at least $400 here. This is what you can control and keep things simple and stupid.
4) I don't like inverter stuff, or variable stuff. So far I am not impressed with residential grade inverter stuff in fridge, in ECM blower, in lowish cost (still expensive like 5k) AC compressor. Same as reason 3 I think most in the industry spend too much money on sales and installation but not enough on the inverter reliability and motor quality. I think this is one area we need more improvement and I may change my opinion in 5 years, but so far I'd be conservative and cautious to avoid headaches.