Welcome back, Jono. When we didn't hear any more from you, I figured you had sorted out your problem.
So, first some questions about your workflow:
1. From your description, I can't tell if (a) the triptych was already complete and you are now photographing it, say, for a catalog or for advertising, VERSUS (b) you are in the process of assembling it yourself from scratch and the final result will be a triptych consisting of three photographs. Which is it?
2. When you photographed the individual panels, was the lighting absolutely constant over time and uniform from point to point? If it was, why are you getting these variations in color and tonality?
3. When you did the raw conversions, were the settings all the same, or did you have to adjust the settings for each because of #2 (the light wasn't constant or not uniform in space)? I'm trying to determine if your fundamental problem is in the lighting and photography or in the processing.
T