1. I'm not a fan of Hi-V. Lowers SEER considerably and lowers capacity. For the same $$ as the Hi-V air handler, you can get a variable speed AH that boosts SEER and has constant low speed fan for circulation & filtration.
2. I wouldn't think it wise. Hi-V runs about 1/2 the normal airflow and if you start zoning beyond that, you are barely moving air over the coil and will cycle on freeze-stat.
3. How are they deciding that? 4 tons vs 10 tons, that's wild. Ask to see their calcs.
4. My cousin has a large house with standard A/C in the attic. Only 2 supplies run to the first floor cuz her Mom didn't want to see registers in the public areas. The 1st floor stays very comfy in hot weather just from the cool air falling and warm air rising to the 2nd floor. House has 1 3 ton unit, one other bid they got (20 years ago) wanted 2 units totaling 5 tons.
5. Height rise coupled with length could be a problem but overall 50-75' is acceptable for refrigeration piping. Manufacturer's instructions need to be followed carefully.
6. Well insulated garage ceiling will keep above it very comfy. Heat as you would any other living area.
7. Are these indirect tanks heated by the boiler? You need considerably less storage capacity than with conventional tanks. 269 first hour recovery is more than 4 standard 40 gallon tanks. That is a lot of hot water!
8. Look into electric radiant for those small rooms. Doesn't use much juice and far cheaper to install.
9. York doesn't sell boilers. Viessmann is the Rolls Royce of boilers. If budget permits, super. If not, there are others for less. Not familiar with the other 2 you mentioned. Buderus is a good boiler.
10. No idea
11. I'd go heat pump. That way in mild weather you don't have to heat the radiant just to take a little morning chill out of the air. Also, I'd guess electric rates are cheap there and a good heat pump would be a fraction of the cost of even a good gas boiler to run, BTU for BTU.