One thing that I did misunderstand in the instructions was placement of the serial buffer. It needs to be wired between the "receiver" board and the Commander board, not after the board then to the tender tether.
I normally wire the serial buffer right at the R2LC socket, and then use it's serial output to drive the Cruise Commander M. That gives be a certainty of having a good signal to the CC-M. If everything else was working before off the serial data, it should still continue to work as the serial buffer presents almost no load on the R2LC output data pin.
Also, per one of John's posts in a related thread, it appears you shouldn't use the "green wire" on the Cruise Commander M 10 pin connector to drive tether.
There are at least two versions of software for the CC-M, one outputs serial data on pin-2 of the 10-pin connector, the other outputs "duty cycle" on pin-2. "Duty cycle" is a signal that just pulses when the motor is moving, it's intended for diesel installations to drive the Railsounds 4 prime mover ramp up and ramp down. Obviously, the CC-M that outputs "duty cycle" can't be used to repeat the serial data. If you know you have serial data on pin-2 of the CC-M, it's fine to use that to drive the IR tether.