Nafraf,
Very impressive system. I've been working on the same thing, mainly to do 3D reconstructions. I recently ran into the problem of switching between the USB remote mode and reconnecting with CHDKptp, which is how I found this post.
Would you mind elaborating on how you are doing the switching with your electronics?
I've worked on 3D systems with multiple cameras now for around 3 years. Any chance I could get a set of photos from you to play around with doing reconstructions? I have the same cameras as you and would love to be able to see some results without having to build my own system first. I visited your website and if you want to do more 3D scanning I'd be happy to help.
Thanks