You won't get oscillating ditch lights with the ERR Cruise Commander, it doesn't have that capability. Getting them to simply be on won't be a big issue. I don't have an Atlas here to look at, my take would be to trace out the wires to see what they power.
Many times for lighting, I just remove the existing interface boards and do the lighting to my specifications.
The symptoms you mention for the TAS suggest an encoder problem, many times those are easy to fix. I find a lot of broken wires for encoders for TAS and MTH equipment, that's all it takes to trigger "rocket mode".
With the Cruise Commander, you have three outputs for lighting and/or "feature". Headlights front and rear, and smoke/cab/markers on the 3rd output. These are the same outputs that the R2(4)LC offers, as they come directly from that board.
