The current model is sized to a Mugen cover. The button alignment is off as is the sizing even for a mugen cover, too tight if I remember correctly.
I have not had a whole day to sit and measure-edit-print-test from the last design I posted here which is not 100% correct.
It is easy enough to edit for the standard cover with openscad, just be sure to include a recess for the camera bump.
As for audio/USB the holes were an afterthought and I never really spent much time mathing them out. The idea for the next design is horn like gripping fingers rather than boxing in the N900.
You can also see the plastic buttons need to be downsized to not stick.