OK, today I received the micro-mini USB adapters I ordered off Aliexpress. That was the last bit I needed to mount the Arduino board properly. Because its quite difficult to access the Arduino USB port through a thick layer of MDF I decided to use an adapter and mount that in the MDF, then stick the Arduino on the end of that and screw down the Arduino with a single screw. Hey, I'm not lazy, I'm efficient!
It may not be pretty or professional but it sure works for me! I now have a flush-mounted micro-USB port!
To celebrate this laudable achievement (ahum) I uploaded some pictures of the insides of the project. I'm not saying you should do it my way, I suggest you do it better and send me the pictures! I'd love to see the results from some of you real crafty folks.
The pictures show all the detail you need to see of the Arduino and sensor mounting, the LCD screen pillars and a bit of the front panel with it's switches in place. The wires are colored making it reasonably easy to track where they go, but I suggest you follow the schematic to see what goes where! I swear I followed it to the letter. The 47uF capacitor is an SMD type I soldered directly to the bottom of the LCD circuit board, so that isn't actually visible. Other than that you should get a pretty good idea of the total project from the gallery.