That's a big old bag of worms right there, I have no idea how you are going to align that back up, best guess would be to fit the bulkhead but there is so much play in the bulkhead fixings it would never be right, same as the front wings.
If anyone here is in the process of a build and has not fitted their bulkhead yet you might get lucky.
Or you could wing it, you must be able to see where the old ones were , tack weld the new ones on, manoeuvre them into a reasonable position then just ensure they are exactly the same on each side before welding them up, that's probably the best way, trial fit the bulkhead before welding them properly.
When you fit the bulkhead and wings there are shims to take up any inconsistencies and align things properly, its all adjustable, its a royal pain in the arse too so having these anything but right could make that royal pain in the arse a proper pain in the arse.
Thinking about it though, it could be worse.