The fist cut I need to make is for the connector plate on the back. I could have spent a lot of time scribing around each component and making it tight as a drum.... but its on the back and frankly I am not that insane considering I am using hand tools. 

The mainboard was already set on some radio shack plastic stand offs, as I had used the computer before with no box. so I just kind of dropped it in to where it would fit on one side.

I used my calipers and measured from the rim of the box to the top of the Ethernet jack (the tallest connector on the rear set). I then used my calipers to scribe a line on the outside of the box based on that depth measurement. 

I can hear the gasps and mumbles now, keep in mind these things are not some really nice multitoyo set of calipers, they are like some free with coupon crappy ones I dont mind messing up the tips a little using them as a scribe.

Then I found the bottom of the mainboard from the top of the can using the same methods and scribe another line. Rinse and repeat for 4 DE9 connectors, 2 usb connectors, and toggle switch for power