It sounds like you know a lot of what needs fixing which common sense in me says fix them and let a later audit find new concerns / confirm the fixes. The employee part of me says audit then use NCR and CA to fix it and show you are making an impact. If that makes sense.
For the company it matters that the issues are fixed so part of me says fix it as you find it.
For you, as a new employee brought in to manage the QMS, you want to have clear wins to make an impact. By ignoring issues until auditing then going through the CA process you will have successes in your name. You look good. However you are leaving a known issue which is not good.
Hope that explains my opinion clearer. I'm no expert just find a degree of common sense goes a long way.
PS just spotted your location. Blackburn...my old neck of the woods. It's changed a lot since I was there. I'm guessing you could be on the industrial estates around the Brownhill roundabout to Shadsworth road. The side of that road on the town side. Judging by your comment about AS9100C.