Carrier 60,000 BTU 92% Furnace vs Carrier 40,000 BTU 95% AFCU Furnace
The 40,000 BTU furnace is almost certainly sufficient. It doesn't take a gigantic amount of heat to heat an 1100 square foot house, even if the house is relatively poorly-insulated. If your goal is to improve your house's thermal envelope with more insulation and better windows, a 40,000 BTU furnace may even be oversized once you're done.
To make sure, do a quick calculation yourself using http://www.loadcalc.net/. You can play with the variables to see what impact your decisions have on the ultimate heating loads. This tool isn't perfect, but will probably get you within 10-20% of the correct number, which is good enough for your purposes here.
Since you're shooting for a well-insulated house, it would be a good idea to get a two-stage or modulating furnace that is capable of producing variable amounts of heat depending on the load. In the kind of house you're planning to have, one of these will be more comfortable, efficient, and longer-lasting compared to a single-stage furnace.