What did you do with the wire from J2, pin-2? The reason I ask is this is an OUTPUT from the CC-M, not an input. However, you can NOT parallel it with the existing serial data coming from the R2LC, that looks like what is happening in this picture.
The data on J4, pin-2 is not exactly the same as the data on pin-1, it's slightly delayed, and also may have commands inserted to trigger sounds during configuration of the CC-M.
In some installations, the CC-M along with the IR drawbar and the smoke unit & smoke voltage regulator overload the R4LC serial data line. Since your locomotive has all of those loads on the serial data line, that would be my top suspect.
The fix is to use the output from pin 2 to drive the IR drawbar instead of the serial data from the R2LC. You can just disconnect the IR drawbar connection from the serial data and see if the CC-M behaves, that will confirm or refute my analysis.
The symptom of this issue is typically the CC-M takes off at full speed, sound familiar? 
