Hankohop,
I've ran MSD ignition systems for over a decade.
Like Coloradodave mentioned, the setup is the same for nearly all of them. Two heavy power leads, one (+) to battery positive and another (-) to battery negative. One switched (12-volt) source (to power on the unit in basic terms, but must continue to provide power during-after cranking), my preferred method is a toggle or rocker switch hidden in the glove compartment, ashtray, or center console for theft deterrent. Coil wires, they're easy to distinguish. Distributor connection, fairly simple once again.
It was already running, so I wouldn't believe you've wired anything incorrectly. Easiest check would to have a family member or friend verify that the LED light flashes when you apply your switched (12V) source and is flashing during cranking on the ignition box. That would rule out the ignition box at this point. I've had to replace (2) CD ignition boxes in the past, that were brand-new.
Are you using a factory style replacement coil with this system?
If so, you really need to transition over to a MSD Blaster 2 coil (which a member has posted above). I've never ran a factory style coil with these systems.