Ok, after a lot of swearing, a drill and a Dremel, the panel is now fitted.
At the front and back of the case is about a 3-4 mm lip which I've cut to allow for the LCD screws and HDD LED. The same goes for the lid a small lip which was catching on the top screws.
For the Gotek switches i'm looking at adding tapping a thread.
I do have a weird issue in the floppy LED stay on.