After many days of troubleshooting this and many parts swapped out, it was determined that the cause for this is the Lifter base assembly that houses the paper size detect switches. Going into test mode and watching the reaction of the switches when the drawer was opened and closed, I saw that the switches clicked multiple times for just one motion of the drawer closing. This would not allow the lift motor to come on and the message 'tray 2 lifting' then 'tray 2 overfilled'. Replacing the Lifter base assembly took care of this and the machine is now functioning properly.