But once you put the lockdown bar in it sits straight down and hits the coin chute preventing it from closing.

This isn't right, sounds like the lock down bar is not fully latching when engaged.
I had this when I did my Dr Dude and it definitely wasn't finding the "  home " location.
Took some tweaking of the whole locking mechanism by undoing the fixing screws to cabinet and either raising or lowering if you can and adjusting the top brass screws.
Not fun, but then it just seemed to work.