I live in a trailer, so it may not convert to your experience. But, I've got three years experience as a HVAC installer, so maybe some of that would be relevant.
How I did it. Well, I was at a seminar on split system AC, and asked if they had any downflow furnaces. The company had a couple left over, a brand they don't sell any more. So they gave me a good price. I took the van and trailer there, we loaded it all up and off I went.
In my case, the furnace was an old Miller downflow. The duct between the furnace and the floor run was nearly useles, and I'm sure I was heating the space under the trailer quite a bit. Of course, I framed that in nicely, and it's very efficient, now.
As for reccomendations, I'd suggest call half a dozen heating companies. See who makes sense, and sounds like he (or she) knows what she's doing. Look for good manners, no swearing, and no pressure on you to make a quick decision.
While installing a furnace, now is the time to consider central AC. Though, it is possible to install the AC coil now, and come back for the outdoor unit later.
The new 90% plus furnaces seem to be the rage. They take a different flue pipe (white PVC) and also require a condensate drain for the water.
As to brands, I don't have a lot of experience. I installed Heil, Rheem, Rudd, and my own unit is a Luxaire. Which I'm told is a York.
Some companies can calculate the heat load of your house, 100K may be too much or too little.
If you have a generator, might be time also to wire in a transfer switch for the furnace, so you can run it off your generator.
I learned that if you want to get flamed, post on alt.hvac.