If both furnaces are installed in the basement, more rigid duct work would have to be installed, but the lineset and the wiring would shorter. I don't think there would be much difference in materials. There would be more labor. It takes more work to run the duct work up from the basement versus running flexible ducts in the attic. I have no way of estimating this. I would think an extra 2-3 days of labor should do it, but I could be way off. The plans would have to modified. You second quote for the HVAC equipment is $21,850, not $26,000. I like the second quote with the 2-stage furnaces. Remember this quote is for over sized furnaces and condensers. I don't understand why there is a separate quote for gas lines. Is this considered an option? I am not convinced you need a humidifier. You can always get a stand alone dehumidifier later if you need it. The kitchen hood is good if you like to cook.

Obviously you could cut a vent in the top of the wall. Here are some of the issues. The furnace is presumably combusting a fuel - the result of this is carbon dioxide and some amount of carbon monoxide. Now most of this is carried away by a chimney of some fashion. But some of it may not be. I would suspect that in most jurisdictions, this would be a code violation. Now the flip side of all this is that the same thing is done all the time to provide air for combustion in the furnace. I'm not sure that it is ever done in a bedroom however. My immediate thought is that this is not an ideal situation with a problem room so close to the furnace. So I doubt the furnace is ideal - so I'd be concerned about the products of combustion. The right answer of course is to get more forced air into the room. And another thing... A furnace room shouldn't be particularly hot. It is another red flag that there is a problem that shouldn't be ignored. I live in a new house and my furnace room in a basement is really not warm. It is a 90% eff NG furnace. One would think that it would be warm but it really isn't. I suspect you have duct issues creating a large leak. That makes your room cold and the furnace room hot.

dovetonsils, I could be off on my balance point estimate. Whether it is 35-40, or 20-25 (seems very low for a conventional heat pump), it is going to be dependent on a lot of variables. There are two balance points. One is the point where it is more economical to use the heat pump versus the back up heat system. If the back up is resistance heat, then I agree with you it is towards your range. If you are using propane, then it should be at the higher range. If the cost of propane goes up, then the balance point can be changed. I happen to think we are going through a long period of low natural gas and propane prices, but that is just my opinion. The other balance point is the temperature at which the heat loss of the house is greater than the heat provided by the heat pump. Usually that is higher than the economical cross over, but again it is highly dependent on the specific house and heat pump performance. It seems to me air handlers cost about the same as a furnaces assuming they have similar features. Even if the furnace is a little more expensive, the OP will come out ahead if the difference is less than the additional required electrical work. The furnace blower will be used every time the heat pump operates. The part that will be used less often is the gas valve and burner. Not much maintenance to be done. Every 2-3 years should be fine. It will also mean less wear and tear on the heat pump. The other nice thing about having the furnace is that if the heat pump fails, you can heat the house with no problem while you wait for service. It is no fun servicing a heat pump in the middle of a winter storm. I think the OP should get quotes for both options as part of the decision making process. Either option is viable and will work.

Where is this house located and how old is it? Can you describe the three levels and where the thermostat is currently located? What is the furnace brand and model number? There is little debate that two zoned systems will do a better job of even temperature distribution throughout the three levels. But how much better is an unknown. As for statements like "this was the most efficient and only way", and "with my current setup the A/C would be on all the time", are more sales pressure tactics than fact. I suggest you ask the other three companies their opinion on installing two systems instead of one. It would good if you posted one of the single systems and the dual system quotes for comments.