I know this may not help you now, but when you get it all sorted, and may have to remove the deck lid, don't undo the bolts, take out the pin in the two hinges. That way the deck lid will align perfectly when reinstalled. I've replaced my pins with mm bolts, so taking my deck lid off is a 5 min thing, and realigning is a non-issue.
Now that I think of it, that may help you now after all. Because if you do as I suggest above, you never have to remove the bolts that you have problems with, so if you align with the working threads, you can simply weld the last hole to the body. Not beautiful, but an option.
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