Get rid of the M2ATX, there junk. Pick up a good opus psu that cuts the power to the 5v rail when computer is turned off.
I really doubt that one USB device would drain your battery over night. Most people leave there USB recievers powered so they dont have to wait for a lock everytime they shutdown. Anway, I guess what I am saying is I would suspect a bad battery or something not up to par in your charging system.
In my last car I did, the alternator was way underpowered. It was only a 40amp alternator. Yes that is right, it was an old car and had just enough to power the car and the head lights. Anyway long story short, I add a carputer and every other day my battery was dead. I replaced the alternator with a 110 amp and voila problem solved. My computer was pulling about 15 amps alone, so you can imagine only having about 25amps to power my car was not nearly enough.
I hope this helps and good luck with your install