Fair enough--I'm afraid I don't understand the scanning part, but at this point it sounds like a highly proprietary process, so I take your word for it. I'm a bit confused about what your gripe with CC filters is, they pretty much make them to be used on the rear elements, and that's why your camera has those filter slots--for doing color seps most likely. You could make three exposures, through r-g-b filters and build the filter pack that way. You'd have it made with that vacuum back & easel.
btw--I'm editting this in here--I have this nagging feeling that you're pulling my leg, but since April Fool's Day has come & gone, I'll take one more shot at it.
Something is missing here--I'm at a disadvantage because all I know is you have a process camera--or some sort of aerial/horizontal type camera, or two. You still haven't said *what* the final print is made on. Most people would just go out, spend a couple of hundred bucks on an enlarger, maybe some CP filters or splurge on a dichro head. Throw in a couple of trays and some RA4AT, and you got your color lab on a shoestring budget right there. But no...no...not you, you reinvent the wheel....So, my question here is this: if you're not altering the color of the lightsource with gels either before the negs (at the source) or after it (in the path), then *how* do you make a c-print or an r-print? In my book, this is impossible. So what's the final material? Some sort of graphics film or paper? Are you printing this photogaphically, or by some other means? I keep thinking c-prints and r-prints because you've mentioned these processes, but I think we're talking about different things here....and, uh, the trade secret part bit won't work for me at this point because if you say it's a c-print or an r-print, the only answer I can come up with is that you're waving a magic wand over the print, casting a spell or holding a seance with your clients. The magic 8-ball on my desk here says, this is highly unlikely.
that said--good luck with the patent.