What size furnace does a 3000 sq ft house in La Crosse, WI need?

Notes

• La Crosse designs to -11°F, and that single number drives everything above. Heat loss is very close to a straight line in the indoor–outdoor difference, so a 81°F design difference gives 58 BTU per square foot per hour. The same house needs 91 MBH on a 35°F design day and 190 MBH at −20°F — a factor of 2.09, which is why a national "40 BTU per square foot" figure is useless in both directions.
• Two BTU numbers, and the box shows the bigger one. A 140,000 BTU/hr furnace at 96% AFUE puts 134,400 BTU/hr into the house; the rest goes up the flue. condensing, the common high-efficiency tier. The mistake to avoid is keeping the old input rating when moving to a higher efficiency — swapping an 80% unit for a 96% unit at the same input adds 22,400 BTU/hr of delivered heat the house never asked for.
• Oversizing is the expensive mistake, not undersizing. An oversized furnace satisfies the thermostat in a few minutes, shuts off, and repeats — hard on the heat exchanger and the igniter, and it leaves the house with hot-then-cold swings and cold rooms at the ends of the duct runs. Undersizing costs comfort on the four coldest nights of the year; oversizing costs comfort on all of them.
• Fuel, roughly — and it does not come from the number above. 6,544 heating degree days on a 3,000 ft² house works out to about 1,397 therms a season, 1,984 dollars at the national average gas price. That figure is calibrated against what households actually burn, not scaled from the sizing rule of thumb — and the two disagree by a factor of about 2.5, because the sizing table is deliberately conservative. Going from 80% to 96% AFUE here saves roughly $397 a year against an installed price difference usually in the $1,000–2,000 range, so the payback is a real calculation and not an obvious yes.
• This is a heat loss estimate, not a Manual J. The real one counts window area and orientation, insulation R-values, measured air leakage, ceiling height, duct location and how many people live in the house. A tight new build in La Crosse can come in a third below this figure; a 1950s house with original windows and no wall insulation can come in a third above. Ask for the Manual J before signing — it costs a few hundred dollars on a $5,000–10,000 installation, and it is the only thing that turns the number above into a specification.
• Where the design temperature comes from. It is the 1st percentile of daily low temperatures at La Crosse Municipal Airport, 9 km from downtown La Crosse, over 2015–2024 — the same kind of airport station ASHRAE measures at. The percentile was calibrated against eight airports with published ASHRAE values and reproduces them to within 2.2°F on average. Expect a degree or two of difference from a printed table; that is far smaller than the uncertainty in the house itself.