Alignment of PCB to mounting holes and USB cut out

[ambios]

Hello,

I'm near the end of my design but I have a few pesky items remaining.

1. I seem to have several areas in the design where the sketch references were lost. Is there an easy way to resolve this?
2. My PCB needs to be mated to the top of the mounting surfaces and the holes in the PCB need to line up with the holes in the mating screw holes - sorry it's a round board.
3. I need some help finishing a through hole that will accommodate a mini USB connector/plug. I would appreciate it if someone could make a suggestion for this.

The design is linked here.

Thanks very much!