I'm at a loss here. Since the chuff output of the C-G is toggling correctly, it's obviously not dead. The ONLY thing that is connected to the chuff output should be an input on the R4LC since you don't have the Super-Chuffer. Given that fact, connecting almost anything to the R4LC input between the range of 0 to 5V shouldn't be an issue.
One thing occurs to me. How exactly are you powering the 5V board, and EXACTLY what 5V board are you using? I'm thinking there is a grounding issue with the 5V board. If the 5V board has a full wave rectifier on the input, that would cause the 5V ground of the C-G NOT to be at frame ground, that is a very bad thing. Let's start looking at other things as the C-G is working when it's floating without any ground reference.