The optima's are red-tops (starting, not deep cycle) Deep cycle batteries are indeed made to handle constant current loads (like that of marine apps, where depth finders, electric pumps, etc are a constat load) Deep cycles are NOT made for starting. They are not designed for the high-amperage draw of a starter, they are more for lower-amperage constant drains.
Both the ignition wire (blue) and the VR sensing wire connect to the VR and the alt. The green wire runs between the VR and alt only, while the blue wire connects to both the VR and alt, and continues to the MSD "on" trigger wire, the electric choke, and the ignition switch (as shown in the original wiring diagram, except originally the blue wire was connected to the + terminal of the coil before the MSD was installed)
Everything (that is currently hooked up) runs off the main battery except the MSD. The large gauge power and ground wires from the MSD are connected to the aux battery (as they have been for 6 years). Currently the MSD is the only load on the aux battery. When everything is hooked up, the aux battery also runs my radio, amp, and auxillary lights.
As of now, the only thing I have really changed in the wiring diagram is the elimination of four fusible links, which I replaced with a fuse box and fuses (have not blown any of them yet....10 amp fuses) The fusible links replaced were for the following devices:
1) ignition
2) ignition
3) hazard flasher
4) headlights
Short of some miraculous cure, I am going to re-wire the fuse block to accept the blade-type fusible links for both ignition feeds. I am going to leave the plain fuses for the headlights and hazard flasher. This is driving me nuts because from an electrical engineering standpoint, looking at the wiring diagram I drew up as I replaced the wiring, nothing is wrong (and two of my friends are in their last year of school for electrical engineering, they concur the ignition circuit is fine in theory)
The last two checks I am going to do (again...) are tracing the field wires looking for cracked wires/shorting, and checking all engine bay grounds. My DVM says the wiring is fine (good continuity), but who knows, maybe I am missing something.
Sheesh, how am I ever supposed to try to put together an EFI system when I can't even make simple electronics work right  
-S/6
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