The only thing I can suggest/think of at this point is to reset/reflash to default configuration and beat the heck out of it in various ways and see if it tends to fail whenever CPU usage is high.. or eth0 traffic or.......... Always resetting to default will help troubleshoot though.
~L0G1C
See here: https://forums.hak5.org/index.php?/topic/33215-changing-source-code-and-building-new-firmware/
As for via USB... no not really. You need a USB to 2v-3v TTL.
~L0G1C
Just because the lights don't do what you expect doesn't mean it's not working. Have you tried connecting to the serial port? It's likely you have a console waiting for you...
~L0G1C
How are you calling/startin wifite? Are you passing any parameters/arguments/switches? I know when I first installed it I think it was the -e (SSID) would cause wifite to crash 1-2 minutes into the process.
~L0G1C
Did you try another 12v DC adapter from around the house? You'll need a DC (direct current), center positive and 2+ amps.. something like a external HD, computer speakers, maybe a printer power supply..
I had a similar issue with 3 different MKV units. All of which were resolved with a better power source. I'd recommend anyone with these sorts of issues to first resort to the wall transformer that came with their MKV. If that doesn't resolve the issue I'd recommend finding another 12V adapter around the house/work that puts out 2+ amps OR a 12v battery.
~L0G1C
Which radio are you using? You might try switching the configs around so that you are using the other wlan interface and see if the issue persists.
~L0G1C