OH that poor frame! It looks like someone was taking welding class on that job.. Glad to hear you've got a pro to help you make it right. As far as boxing it in, it looks like the front is done so if you wanted to - you can fill in all the way to the rear suspension points. If this will be a cruiser then I would probably just get under the cab done.

As for the roof... it will be a pita to remove the window and refill the metal (imho) unless you can find a similar year or body style to match it to.

Thanks for sharing the build and the pics.