I'm in kinda the same boat as you although I've done quite a bit of snooping on the forums and in the thread and have not found any answers to my issues. Just to get the formalities out of the way, yes I did a full wipe, and I've wiped each time I've flashed an update to the ROM. These issues have been present on each iteration of the ROM thus far, and was not present on stock.
Issue #1 - Notification LED stops working correctly if device is sleeping, the color works fine and will blink on the correct times to start but after a few blinks it either will go solid or stop blinking period.
Issue #2 - While listening to Google Music or local music with the screen off notifications cause the volume of the music to drop but then not return to the level it was at previous to the notification until you hit the volume rocker.