I too question the 2.5 ton system for a 1,000sqft house. FWIW my house is just a little south of your and 50% larger. Just installed a 2 ton A/C. Furnace is 88,000BTU that came with the house, although 45,000 would have been more than enough. A/C went bad, but furnace still good, could justify replacement just because it was oversized.
When all the facts are spread across multiple posts, and you are following multiple threads, details become challenging to keep track of.
I believe 2 ton 2 stage. Seems a really good call. Not sure size or stages of furnace, but might hardly run as that pump should carry the house to very low temps.