Kurt,
Was up at Alameda at the USCG island for a week working on equipment last week of June. If I have another trip there I'll contact you.
Have not installed the window yet. My floor substructure was rotten and I had to replace it all. It looks like you may have the same issues that I have.
I would check all stringer, transom and motor mounts.1/4 dia drill bit, 1/2 to 3/4 deep, from the inside.
It could also be how the Tee bolts are on the window.
My fuel tank also had holes in it. Had to replace.
Are the hold down nuts loose?
Is there a gap on port or starboard side?
When I'll install my window I can then adjust the gap. Window hold down nuts are accessible under dash and glove box.
This is the trim sender that indicates whether it is up or down. One wire is ground the other connects to the dash gauge. You can back off the large nut, then unscrew the sender assembly.
Also you may want to start you own thread/post on you boat for what you may be planning. It keep all your questions and progress together. If you rip out take plenty of measurements. You may want to decap also, it was a pain doing the under side of the bow. I'll try to correct all my photo links because of the photbucket issues soon.
Glad you posted some upholstery shots I was missing all hatch covers. The rear sundeck I'm going to use multiple pieces of 1/8 to 1/4 inch ply glued together to fit the curved surface.
I don't know if you are going to do my route, changing upholstery panels, switch/ dash panel and glove box. may be able to send some small items that I am not going to use
Also how is that Ski pylon mounted in the rear? May want to do one.