I have had MSD boxes fail with similar results. I have also had an timing chain burp (Jump) with similar results.
The MSD manual can be downloaded here (
http://www.msdignition.com/downld1.htm ) Page 9/10 they have a "Checking for Spark" cheat sheet. ---they also have a customer support line. The other thing I would to check is the quality of the electricity feeding the MSD units.
MSD: Customer Support Department at (915) 855-7123, 8 - 5 mountain time.
The other item to review would be if the timing chain has slipped a gear(tooth) this can be checked by popping out the plugs, valve covers and follow the firing order closely.
--Steve