Hey jblaine, first thanks for starting up this thread. Am I right your car has never started witht he Hydra? If so, I know you mention recharging your battery, but I think you might just need a more powerful battery. I was using the stock battery with mine, and it didn't take much for the battery to lose charge enough that it couldn't start the car (I was running my notebook through the cigarette lighter). I got a cheap but much higher output battery from Costco and it works fine. As you probably know, the sequential firing start of the Hydra needs a more powerful battery to get the car started than the stock ECU.
Just thought it would be a lot quicker for you to try a more powerful battery than all the more complicated stuff you're getting into.