That jig is something else! I'm in awe of how nice a bit of kit it is.
Looks like you've got a fair bit of work to do, but it's such a nice feeling when it's done! You'll definitely want to chop out the sills anyway so you can do some repairs/prevention on the inner sill, I cleaned it all back while it was opened up, and slathered on loads of weld-thru paint, then squirted a ton of dinitrol down there after the outer skin went back on. Very satisfying!
I'll be keeping an eye on your progress!