I'm excited to see how you go with the auto bed leveling! The OEM bed is more crooked than Donald Trump! :-P
Yes, the original z603-S blue board had a completely different pinout, so I had to do the whole pin reverse-engineering twice to get a new marlin build running. The original blue board came with a really old version of marlin and would crash randomly half way through a print... was very frustrating. I spoke with JGAurora and they refused to release the source code, which is breaking the GPL agreement, but they don't care about that at all....
Anyway, the green board is much better, and has much better drivers, and better cooling for the drivers too.