I'm actually working on one of these too myself...
http://www.sega-16.com/forum/showthread.php?t=3596
Mine will use IDE ribbons to connect the cart lines..
the difference on mine however is that I'll be using a single power supply, not two.. I also am thinking of adding Composite out directly from the console, and Component video (via the JROK adapter). It would be a perfect combo, without any special cables..