BUT are you CHECKING that the small red has battery power in both situations? This could be a simple and well known "problem" (easily corrected) in the original car wiring.
When you twist the key to "run" the IGN1 "run" line supplies power to the ignition system, alternator field, and VR and on some models a couple other things
THIS POWER IS ONLY LIVE with the key in the "run" position. This power GOES DEAD when the key is twisted to start!!!
HOW DOES the ignition get power in "start?" Through the IGN2/ coil ballast bypass circuit. This wire originally hooked to the coil + terminal on the ballast, and with the key in "start" fed power to the coil. YOU MUST jumper the IGN1 "run" and the IGN2 "ballast bypass" together when using a non ballast ignition such as MSD.
Another little tidbit. Make absolutely certain that you have NO connections to the coil At ALL except the two wires from the MSD box.