Just paint the wood white on the window wall,the Windows should blend into the wall .

Well the sandiing had to rear it's ugly head sometime! Sand them down and paint them either the wall colour or white to match the windows to make them blend in. I'd also do the other room the same and the doors, other wise you're still going to look like you have two different styles. Everything all the same or not at all.

You'll make it look a lot more spacious by toning down a good proportion of the wood. I'd do the Velux's too.

I've seen this 'orange' finish on new builds. Not the nicest colour. I'd sand it off and start again. Do it at this stage because if you don't you'll just keep looking at it and wishing you had.

Sand it off and start again. It won't take long if you use a sander.

slightly off your question, but are you thinking of curtains after the work is done? Might be nice to add some privacy and to soften the room!