Yes I'm not really sure what to suggest either! It sounds like it should work fine.
Def try uploading the MOCO firmware again.
Make sure the connection on pins D0 and D1 is clean. If they have a dodgy solder joint (eg going to 0V or 5V), they will block all data coming through the USB. You could even chop those pins off to be safe.
Can I confirm the jumper is off of the ISP connector (for MIDI mode). You put it on for Arduino mode.
I assume you've loaded all the miniAtmegatron libraries and sketch from here: http://soulsbysynths.com/miniatmegatron-downloads/
(not the Atmegatron page)?
Umm... I'm not sure I can think of any other suggestions at the moment.
If you want to prove that the serial is working, you could try uploading the SerialCallResponse example sketch in Arduino. (make sure the shield is off when doing this)