Kev, I had a similar box mount issue and have done as Brian suggested-still to road test though, but should be better than before.
Sounds like you're all geared up for the job of checking for straight, I ended up dropping mine into Dave Kellet (frame straightener)at Springwood, with the drawings, as my back end was pushed to one side a few mm, and front downtubes out of whack, which is why I couldn't get the wheels to line up.
Good luck, I can give you Daves' number if you need it