I'm just spitballin' here: They do make 6v to 12v DC-DC converters. Consider driving your ECM only with one of these (there is one on eBay for <$20 that can drive 4A/48W load - you'd have to check the current draw of your computer/injectors). It says there is 40mV of ripple on the output which may or may not cause problems with your ECM. I'd put a large electrolytic capacitor on the output of the DC-DC converter if i were to try this.
I put a GM TBI system on a small block in a Camaro i built, and all of the sensors (there are only 5: IAC, O2, Temp, MAP, throttle position) were driven/monitored by the computer, so if the computer was running off the 12v then its possible the system would work. A multiport injection system may need more current, i don't know.
you could try the DC-DC converter idea before going to your twin 6V battery approach which should also work.
