Todd:
For instructions on checking MSD ignition box, go to:
http://www.msdignition.com/
and select Troubleshooting from the menu. They have instructions on how to check the system safely.
Also, unless I missed it, you never stated what type of distributor you are running. If it is the MSD billet unit, you may wish to ensure that the centrifugal advance mechanism is functioning correctly. I had one which I purchased about five years ago. After about 12 months, I started having serious starting problems. I talked with the MSD folks and they told me that they had tried a different anti-corrosive treatment on the advance mechanism and it simply didn't work. My weights had stuck at full advance and wouldn't retract, preventing the timing from retarding at low rpm. This would result in exactly the symptoms you report; runs fine at high rpm but runs poorly and backfires or dies at low rpm. I returned my distributor to MSD and they replaced all of the internals under warranty even though it was not still covered (Kudos to MSD, BTW). Just a thought here.