Re: Total Rebuild Help
If the window doesn't close now, you want to brace across the hull w/ a 2X4, helps prevent cracking @the consoles from the stress of sagging. If it will be unsupported by deck ply for a while, I'd also add temp bracing down to the hull.
If you're shoring up the hull braces & pulling the cap again, 2X4 across the consoles & support the cap as best you can until you're ready to put it back on.
Bending & flexing the cap as you handle it removed from the hull makes more work, so a few screw holes thru it, screwing it to the cross brace is much less work. Just be sure to use fender washers & or scrap ply to prevent cracks as you screw thru the console.
If it wasn't as bad as you thought, do you think it is still sagged somewhat?
Or as GT said in an earlier post, the hull may not be as symmetrical as you'd think it should be. Now w/ the cap on it's harder to tell, but you want to try & do the best you can to prevent glassing it in misshapen.
EDIT: Or put another way, what GT said ^^^