Sounds very familiar, last year I dropped mine off at the body shop and was told 5 months, 11 months later I got the car back "almost" done, still need to take it back to be finished up (inclusions and unfinished details). I hope you have much better luck than I did with the time frame. See my thread titled "68 goes to the paint shop" if you want to follow my journey.
As for the window cranks, slide the tool in between the handle and the panel (or plastic thing if that's still there) align the tool with the handle direction, eiher directly underneith it or directly opposite the handle depending of which direction the clip was put on, then push toward the center until it pushes the clip off.
Aftermarket body panels don't fit worth a crap, your bodyman will have a lot of work going that route. Try going to swap meets and scouring this site and Perfomance Years forum under parts for sale. You are right the 68 deck lid is a one year only deal, hard to find and expensive. I have one that's a little better than yours but it has some rust holes clear through the corners. I have heard nothin but bad about aftermarket endura bumper replacements, ty hard to find a good one or fix the on you have.
What color are you going to paint it? Looks like it might have been Springmist green, that's a beautiful color.
Good luck and keep the pics coming.