So the 2 furnaces are next to each other in the basement/lower level? IF so, on simple fix might be to leak-lag the furnaces and tie the ductwork together and add back draft dampers. I suspect one furnace and the 5 ton AC can carry the whole building. I think one pro on here once said they've never seen a undersized furnace. You'd have to be massively undersized not a ocarry a space over a 24 hour period.
One thing to remember, the larger the home, comparatively more thermal mass and less surface area to volume ratio. Also being 3 stories, you have a proportionally smaller roof as well compare ot a signle or 2 story home. A 4000 sqft home will never use nearly twice the heating and cooling as a similarly designed 2000 sqft home, and far less than 4X a 1000sqft home. A typcial 1600sqft home might onl need 2 tons and 50k BTU's, while 4 tons and 100k BTU's can carry many 4000 sqft homes.