[Kurakka]

Don't know if this is any help. I have seen this type of issue show up on computers that have bad USB ports on them, the device you remove still shows up as though it is still plugged in. You say it works on Stock rom and past that point I have not figured out a way to test the USB port on the phone other than to use it as a disk drive. If all that works I can only say that the unit does have a faulty part, I agree that perhaps a replacement unit might fix this. Another option would be to use the Stock ROM for about a week to see if the issue doesn't show up. Perhaps the Custom ROM some how expedites the issue to show in a shorter time frame.

Like I said don't know if any of that helped.