Don't be so quick to discount the value of original windows! Besides looking infinitely better than any replacement window in an old house, re-working your old windows is actually the financially and environmentally responsible choice. Yes, in poor condition, they can be quite drafty and inefficient. However, in good repair, they can be as efficient as the best windows on the market today (and almost always more efficient than replacement windows). My rebuilt 1770's windows with storms installed radiate a heck of a lot less energy than the top of the line low-E Anderson's installed in our 1994 addition, and will last easily another 200 years, whereas I will be replacing all of those Anderson's within the next 10 - 20 years.
Definitely look into a weatherstripping those doors, preferably with interlocking metal weatherstripping. Check out Killian's (local) or Accurate Metal Weatherstripping (web). Draft sucks more heat than radiation, in old houses.
On the wooden lintel, some argue (with very good reason) that this is technically an "alcove" installation, and as such alcove stoves and clearances must be met. On the flip side, there are countless (in SE PA alone) stoves residing in old cooking fireplaces, violating the clearance requirements to these wooden lintels. I know one of my stoves is closer to the wood lintel than I would have allowed if I were doing the install myself, but it was cleared by the building inspector (new addition) and 20 year's worth of insurance agent inspections, and has never been a problem. Not the greatest of reasoning, but it's where we are.
As to heating the room on the other side of the fireplace wall, it might have some merit. My stonework runs about 85F on the fireplace, with the stove going 24/7. Even on the outside of my house, the heat signature is quite clear. The photos below show the outside walls behind each of my fireplaces containing stoves. The one reading 38F is an 18"+ exterior wall, and the one reading 50F is just a summer kitchen fireplace wall, likely thinner than 18".
Do note the old windows with storms in the first photo are black (~14F), whereas the newer low-E dual-pane windows on the new addition in the second photo are reading close to 30F. The few warm windows you see in the old part of the house had missing or damaged storm windows, at the time I took those photos.
So, you will push some heat thru that wall, if you keep the stove going 24/7. Not sure how much, but it's something.
Watching the folks on this site in my first few years, heating small and tight houses 100% with their wood stove, I got excited about doing the very same thing. However, I was ripping thru wood at a pace of a cord a week, and we were still cold, trying to heat a very large old house. More recently, I just keep one stove fed 24/7, and only keep the second stove going when I'm home for weekends (and holidays). This keeps my wood usage manageable, adds a lot of BTU's to the house (keeping my oil bill down), and removes a lot of the stress of keeping the house warm. Yes, the boiler runs as dictated by my programmable thermostats, but a heck of a lot less than it would if I weren't pumping BTU's into the house with the aid of a wood stove.
As to your floors, I'm sure they're beautiful! I grew up with some very wide pine floors, but this house has floor planking all less than 10" wide. Apparently, it was a sign of wealth to spend the extra coin for narrower floor boards, back in the 18th century. So opposite our thinking today. In any case, have you considered insulating from below? We have the oldest part of our basement finished, and have 1" foam board with drywall fitted to each joist bay. It's not good enough to keep the floors completely warm when we let the basement cold, but it does eliminate all draftiness.