Hi I just bought an older 2,500 sq ft home in zone 6, SE Wisconsin. Currently there is boiler heat and a couple of window a/c units. There is no duct work at all. The home has a flat roof over the front part and a combo flat and peaks over the rear. The exterior facade is falling off and the windows seems to be done as well. Everything pre dates the previous owners who bought in 1979. My plans are to tear off the old roof in back, build up the walls to be the same height as the front, and put 4/12 or 6/12 trusses front to rear in one continuous roofline. With this attic in front, we can have a/c added to the 3 bedrooms and well as add more insulation. In back the attic will be quite large, almost a living space. In there we can add a/c and upgrade the insulation. Maybe some area with plywood flooring and lights for storage too. We are also going to get new windows(don't know which ones yet) and vinyl siding. I have numerous questions about all this, but I'll start with my HVAC. I have a quote to add a Mitsubishi MrSlim with an air handler over the upstairs in front(under the new gabled roof), a wall cassette in our master on the middle level, and another air handler in the new rear attic handling the rear of the house(single story). This is quite expensive(around$15K) and still leaves me with a 40 year old boiler. I could get a new hi efficiency boiler too, but now I'm in over $20K for HVAC and over $100K for the entire deal. I hear the new mini splits do a good job at heating now days. Could I get away with just the mini system? If the house has been wrapped, new construction windows, air sealed in attic and upgraded insulation? My other idea is a conventional forced air and use the new attic space for ducts and such. Ideas? I have attached a pic where I superimposed the new roofline.

The picture

no, lets start with the insulation because the boiler questions can't be answered until you identify what the building envelope will be. Since you need new siding and are adding on, you must be aware that this is the exact best time to upgrade your house to around R40 walls and R60 roof and air seal it well. (These are rough benchmarks)

Yep, pick an insulation and air sealing target. That will allow you to make an intelligent decision on heating and cooling appliances... He is exactly right that with the re-roofing and siding, now is THE best time to upgrade the insulation. Doing that will probably also allow you to use smaller less energy intensive HVAC...

If you were to replace your boiler and water heater with direct vent appliances it would practically eliminate the concern about back drafting from a stronger radon mitigation fan.

So once they scrape off the fake stone and stuff from the exterior down to the plywood, how do we upgrade the insulation? There is still drywall and paneling on the inside and plywood on the outside? He said he would use the Tyvek wrap.

(Who is "he"?)
You can install 4" of polyiso (two layers of 2") on the walls over the plywood, then strapping over that - both to hold it on and to give you something to nail the siding to. I'd strongly suggest taping the plywood first, as that will help you air seal your house. You can buy new polyiso, or recycled polyiso, which is substantially cheaper. Doing this in combination with a few other insulation upgrades will allow you to use ASHPs (mini splits) to provide both heat and AC, plus make your whole house far more comfortable. And by adding solar panels, you can head toward never again buying fuel for the furnace.

Sorry Bob, "he" is a contractor I spoke to about the job. If the walls are now 4" thicker than previously, would the windows look funny or sunken in?