all the wiring is checking out fine though. Like i say, the brown wire in the right side of the ballast that is the bypass wire does indeed send all 13 volts to the battery in start mode, but only when its not combined with the 'run' (left side, blue wiring) of the ballast. For some reason when combined, weather through the ballast or directly jumpered together, it makes the 'start' voltage drop to 10.5. Very weird, like each side messes with the other. If each side is separated, i get 13 volts on the 'run' side, and 13 volts when cranking the key to start on the 'start' side. but again, when they are attached either by straight jumpering, or through the ballast, the run side makes the 'start' mode drop voltage to 10.5.. Makes no sense because on the bypass side of the ballast (start side), its a straight shot to the coil and it does shoot the full 13 volts to it, but when its linked with the wires from the other side of the ballast, thats what gets it.
Only thing i am NOW questioning is this..I just was looking at a diagram on the web and it says that:

Ignition 1 has power in BOTH run and start. Feeds the coil+ through the ballast resistor at reduced voltage.

Ignition 2 has FULL battery power ONLY in START and is a bypass circuit to send full voltage directly to the + side of the coil to increase voltage output for starting.

ok, ignition 1 has power 'BOTH IN RUN AND START'

On mine, the voltage on the RUN side goes dead when in start mode, It toggles back and forth. So when the key is in RUN, it has power from the bulkhead as its supposed to, BUT, when cranking the key to 'start', the power from the 'run' circuit goes to zero and the 'start circuit' powers up, then when i release the key back to run, the 'run' side power comes back. SO, which is correct, the way mine is doing or what i read? If there is supposed to still be power in 'RUN' at the same time its in 'start', then this is a problem because like i said, with mine, its either run or start..I think they are probably wrong and the power on the 'run' side is supposed to go out the bypass 'start' circuit powers the coil..but i may be wrong...