If the basement is finished, it will need very little to heat and virtually nothing to cool it. If the home is fairly tight and well insulated, and has osme shade, it takes very littl eot heat or cool it. Those numbers sounds very plausible. You summers are more humid than hot and winters are not too cold. Looks like they used the correct design temperatures for your location.
I have no reason to doubt hte manual J. Looks like downstairs was right between 2.5 and 2 tons. Since it's humid there and you have 2 systems, I would have gone 2 tons personally downstairs. Better just a little small than a 1/2 ton too big. Manual J has some safety margin already in there.
Upstairs... well, well 1.5 tons would be plenty if the ductwork is well sealed, insulated and installed correctly. The latent gain however seems really ,really low. It doesn;t factor in revserse stack effect, showering, occupancy and other normal factors. I think you're probably closer to 2 tons upstairs.
So my summary...
2.5 tons downstairs, not great but OK.
3 tons upstairs... Way oversized unless it leaks a lot of air and you have a lot of unsealed can lights, air leaks, etc. Otherwise 1.5 or 2 tons, but I'd have a new manaual J done factoring in air leakage and occupancy. Keeping mind that most air leaks in summer are upstairs.
The furnace is an absolute monster. That's rediculous! More than 2X what the load calculations call for. I could see 60k BTU jsut because it's a 2.5 ton AC (2.5 tons is pushing the limits of the blower in a 40k BTU unit).
AM I suprised at what was installed. Aboslutely not at all...sadly. That's what you get these days in new construction... where low cost wins over quality and proper design and installation... especially tract homes. SOrry you have ot learn thsi the hard way. I think for more Americans, ignorance is bliss. If you don't know how a properly designed and isntalled HVAC system is supposed to feel, then you wouldn't know better.
I've drastically downsized all the equipment in my home and made my wife a believer. She didn't know a furnace and AC system could be quiet and every room could be the same temperature. She figured that's just what you lived with in most homes.
From a building science perspective, there's no excuse, for any home over 2500sqft to need more than 20 BTU/sqft heating and 15 BTU/sqft cooling. If it needs more than that, its' not designed and built right. We have mpg limits for cars. Why not energy performance for homes of different size categories? We have insulation standards, but that doesn't nessesarily deliver. It would be like having aerodynamic drag limits for cars, weight limits, then having seperate fuel consumption testing for crate engine on a dyno. It's not until you put it all together that you really know what the package is.