Hi Chris,
Have taken some pic's to show the alignment we have ended up with. Not saying it's right, but it was the best we could get without major surgery. I think I am happy with it, see how it compares with yours.
Rear body blocked in place - now bonded as seen.
Passenger side front sill end.
Drivers side front sill end.
Drivers side rear sill end.
Passengers side rear sill end.
Hope this might give others some ideas, even if it is just to say where we have gone horribly wrong.
Good luck with your bonding,
Paul D.