I hesitate to make this comment, since it sounds like you are too far along, but perhaps it will help someone else. This problem is one of the reasons that we decided to do a geothermal system. I know of a historic style house (a Deerfield house to be exact) that was built in the 80's with a geothermal system. When the well went dry during a drought (it was an open loop system), the homeowners put in AC condensers. It totally ruined the look of the house. There was no good place to put it and it was noisy. Their experience made me think about the placement of units and ultimately decide against them. My story does have a happy ending. Incorporating geothermal into my new build inspired the owners of the Deerfield house to redo their geothermal system and the ugly units are gone! They are back to beauty on all sides and no racket.

Near a return vent is a good location, but thermostats can be installed elsewhere. Or you can use a wireless system, keeping the receiver in the ideal location, but which you can access for adjustments from several places in your home. Here is a link that might be useful: Wireless Thermostats

Perhaps you live on the sunny side of the building, over the boiler room, on an upper floor (where all the heat rises to - and perhaps getting all the heat from the roof). Get a larger unit. If your unit is all broken up into separate areas, and then fans would be needed to get it to other areas.

From your description, it sounds like the glass wasn't properly blocked when the glass was set in the frame. As long as the insulated glass units haven't failed (fogged inside), a glass company should be able to re-set them. What they have to do is to break the seal between the glass and the vinyl frame, properly block it on the bottom and the sides and re-seal the glass to the frames. This is somewhat labor intensive but you may not need new windows after all. Good luck!