ST-2E to NCM-300 - Extra wires

[ajcast5201]

Hi everyone,

After reading other experiences regarding the upgrade from the ST-2E to the NCM-300, I decided to give it a shot myself and save some change. I've received the new controller and am accounting for each wire on the current setup, as I understand it to be a 1:1 swap.

On the thermostat side, I've had no issues matching wires. The same can be set for the damper motors. However, when looking at the transformer and system areas, there is what looks like a jumper Transformer 1 to System R. There are also two wires in Transformer 2. Additionally, there are two wires in System Y. I've attached pictures.

Full transparency - I had someone install two Nest thermostats, and they were able to work by adding a jumper to the O/B ports on the right side of the ST-2E (I have to switch the wire when changing from heat to cool or vice versa).

Thanks in advance. Looking forward to learning more about thermostat wiring.