Okay. Please excuse my earlier reading comprehension failitude. Now that I've had the requisite amount of intravenous caffeine, I think I get what you're about. I'll try and express it in my own words - tell me if I'm getting warm.

What you're proposing is essentially the same as building a scratch-built, homebrew computer, like those linked off the 6502 thread, and a homebrew OS to run on it. Except that you want to do it in software, rather than hardware.