Like Bird said the glass is too cold vs the inside heat.
You have too much humidity inside the house. Get rid of it.
Not much you can do in the cold weather to fix it.
Use the dehumidifier in the living quarters and consider getting a bigger/better one. Get humidity down to at least 30%.
A/C is the best dehumidifier and we get out around 20 gal/day water down here but that won't work in cold weather up there. We have the same sweating problems when someone cranks the air down to 65° and the ambient is 95° with 90% humidity, but it clears up here once the a/c sucks all the moisture out.
It is cheaper to heat dry air than humid air.
Power vent attic, showers, cooking.
Try a test, if possible by taping some heavy visqeen to the outside of the windows in 1 bedroom as airtight as possible. That should raise the inside glass temp to overrcome the dew point.
Your new entrance door sidelites are just better units than the bay window etc. Test the glass temp with your IR gun.
Your last concern is mold growth and rot. Be aware that the white colored stuff that looks like dust is more dangerous than the common green stuff.
Here is the best caulk I have ever found. Lasts forever.
http://www.npcsealants.com/900.htm
It was 59° here overnite and I'm pissed because I had to wear long pants this morning.
