Unfortunately, I don't think there is a cure for this (besides ripping the rear chassis apart and starting again lol). It was common fault on most Novas. You'll rarely find one with a beam that isn't offset. My Mk1 shell is like yours - all the trouble came from the drivers side outer arch, no trouble on the passenger side though. The Mk2 shell I have is offset to the passenger side instead. I guess I can't win lmao.
What offset are your 16" wheels? Just wondering if they might be less than ET45. I had 15" TSW Evo R's (ET40) on the Mk1 and on the passenger side, there was only about 2-3mm between the inside of the tyre and the inner arch. I'd imagine that with ET45 wheels, it would've rubbed constantly!
Cheers,
Kieran