CAPPilot.. I have a ser-2 and am using the dz2001A data driver. make sure the wye cable is connected legacy plug to legacy base.
and the tmcc base to base plug on the Y plug.
the Y cable serial plug gets connected to the ser-2 db-9 plug
the other PDI cable end goes to ser-2's input.
unless I'm incorrect you no longer need to use the manco booster as this is what the ser-2 is for so all you need do is connect your db-9 going to other daisy changed lionel devices into the ser-2 db-9 output connector or you can iuse the 3 wire screw connectors for Dat/Com connections.
after legacy base 3 light sequence ends the yellow light will blink once every second.
hope that helps you as this is how mine is setup and works flawlessly.
a side note I had an issue with the ser-2 and a dz 2500 switch machine that was in a jammed mode showing red light and in attempts to fix it the dz 2500 was energized constantly end result it took out my dz 2001A data driver!
to all if you hear the ser-2 chattering and its a loud chatter run to your power switch or ? and kill power to entire layout as this is what I heard when my switch motor would not kill power at end of throw to curved route.