I am not touching the BTU/hr thing with a ten foot pole until the chemical engineers are done with that little rabbit hole.
To the OP, my current home (way up north) is tight as a tick with no ventilation. My next home is going to have an HRV, or maybe even an ERV (had to look up the difference) but my woodstove in the house with and HRV/ERV will _definitely_ have an OAK (Outside Air Kit).
My OAK will be connected directly to the air intake on the woodstove so there will be zero issues with the HRV equipped HVAC system unless the loading door is open.
There is no good reason (in a tight but ventilated home) to feed conditioned air to a woodstove for combustion, and it makes the HVAC system harder to balance. In my current 1980 build where I am dealing with mold issues, not having an outside air kit gives me some air flow. My current home is basically Heated with no VAC.
As far as the two floors, I would plan to keep the basement about 10 degrees above the dew point with whatever your primary system is (oil? NG? electric? etc...) and put the wood stove on the same floor where you and your family spend the most time. If you spend most of your time upstairs and the 28' chimney is measured from the basement floor you can probably just plug and play any number of stoves on the upper level without excessive draft.
Trying to get 100,000 BTU per hour out of one stove for ten hours is 1,000,000 BTUs loaded in the firebox, about 1/18 of a cord of spruce or a 7.1 cubic foot firebox. If you have unlimited access to mixed oak (Quercus sp.) you could get away with a 5.1 cubic foot firebox. Not gonna happen. You could get two wood stoves in the 3 cubic foot firebox range, and feed them about a cord per month in your heating season. That will get old very quickly. I burn a touch over a full cord every January and it sucks donkey parts. Feb first is one of my favorite days on the calendar, because my wood consumption is decreasing.
FWIW my oil fired boiler (hot water baseboard) is rated at 100-120 k BTU/hr depending on what question you ask, my 3.0 cubic foot firebox woodstove is rated around 50k BTU/hr max, and my home is tight with 2x6 walls, fiberglass batt and vapor barrier. I have roughly R infinity in the attic with blown in. At -45dF I am loading my stove three times daily, the boiler is at max duty cycle, but I am maintaining roughly +80dF on the upper level (I have 1200 sqft up and another 1200sqft down, stove is upstairs) and the wife is still in summer clothes. At -50dF I have a hard time maintaining +75dF upstairs with the wood stove raging on three feedings daily, and at -55dF I get concerned about the power going off and the pipes freezing in the crawlspace. During previous power outages I have calculated I have 8-10 hours to get my generator hooked up and the boiler running again before I have frozen pipes at -55dF outdoor ambient, incoming potable water is at 110psi . The pipes for the hot water baseboard are glycol'd for -70dF.
A 3 cubic foot firebox with adequate dry fuel made a very pleasant dent in my oil bill. I was buying about 1500 gallons per year before the wood stove went in, now 800-1000 gallons annually since 2014. 500 gallons minimum savings, I saw heating oil (cash and carry, not delivered) @$4.47/ gallon this week.... $2200 per year savings, plus you can cancel your gym membership....no brainer.
On the one hand you are in a new home "we just built it," but one the other hand you were running a wood stove last winter. What was your actual energy consumption last winter (oil + electric + natural gas + solar + cordwood and etcetera), and was the house as warm as you wanted it to be?
I agree with begreen you should start looking at stoves with a firebox of size of 3 cubic feet and up.