I don't know about the signal path to the lower board. I looked over the schematic for a minute but it wasn't overly clear. I'm not really experienced with digital electronics.
Last night I left the board on for a few hours and came back to it to see if it was acting weird. Everything was fine except I heard a couple isolated blips again in 5-8. They were still very infrequent when compared to having U164 removed. So whatever is causing these blips is more pronounced when something warms up. There must be something wrong somewhere. I've attached some small clip of u164 in and out to this message if you want hear what these blips sound like.