I think Tollycraft made a fair number of the 40' tricabin, obviously not as many as the smaller boats like the 26 obviously. Our 79' has a single double berth on the starbord, it could be made wider, say a queen width (not length). I've seen them with crosswise queens retrofitted but personally I don't like crosswise berths in a boat since it seems you're always listing a bit one way or the other.
Our boat it was built with a desk/vanity on the port. It makes for a very roomy and nice master. However I think this could be shortened to add a washer/dryer unit just aft of the hanging locker (assuming it's a combined Euro sized unit). All of them have the 'tunnel' for the exhaust piping.
I'm not sure why you'd want to get rid of the windows. In many of the boats we looked at before buying the Tollycraft, one of the problems was the 'dark hole' after cabin with poor natural light.