If the installation manual says three inches, it means three inches. If there is only a one inch clearance the inspector should have withheld approval until it was corrected. If there should be a fire caused by failure to adhere to the mfr's specs someone's butt will be on the line.

That's the XB90 furnace, Trane's low end entry level high eff condensing furnace. Lots of BTUs for a small space. Furnace surely would be oversized. What is your location? Attic location could be problematic for a condensing furnace not to mention the length of the lineset. No way to shorten distance by locating outside condenser to another site? Pricing includes new AC condenser, evap coil? If so what models? IMO

Where milder/less mild matters is in the heating season with a heat pump. The AC functions about the same, but if it's too cold out the heat pump BTU output may not be enough to keep up. Even if you have plenty of AC capacity in the summer. I assume you're on NG and not propane. Also, $2.1 per hundred cubic feet (ccf) would be more normal. Ours in ATL is around $1/therm (therm = ccf), and it might be $2.1 once you add on the administrative costs. It might make sense, if you're already paying the overhead on your NG account, to go with a dual fuel system. The extra use spreads that admin cost further, if your system is set up to do it when it makes sense. A dual fuel system will run the HP until it can't keep up (or the controls lock it out based on outside temperature), then kick on the gas furnace as the 2nd stage. This takes advantage of running the heat pump most of the time without needing electric heating strips as backup heat. The HP will put out about 3X as much heat as the energy it uses- that's what makes it cheaper to run than a NG furnace. But the backup heat strips are 1:1 on energy to heat, which usually isn't competitive with NG. Also, I kind of like the idea of having a standard efficiency gas water heater. Offends my drive for efficiency, but as a kid on the N end of AL, the power went out enough during hurricanes, ice storms and the like that it was nice to still have hot water (and a fireplace) when that stuff happened.

Since the walls are rocked, it's a little late to address changes in the duct system. Hopefully, manuals J & D were addressed to optimize your system. You should inquire as to the type of furnace (number of stages). Model numbers would be nice. Since you have a large house, how will a single stage unit handle things if only one zone is calling for heat. Is there a dump zone? Would a third zone give you better control? Unfortunately, the best time to address this would have been at or before signing the agreement of sale (after doing a lot of research). Now, you're kind of at his mercy. How about air conditioning? Other home qualities are excellent (insulation, windows, slab heat for basement). If basement is to be air conditioned, will need to have controllable supply and return registers (off in winter). Good luck with your home. V