The MSD box WILL retard timing over stock control module. A MSD 7AL3 is about 4 degrees retarded from a MSD 7AL2. I've seen that first hand plenty of times from dyno tuning (Dyno box) compared to the car's ignition box. I would bet it's even more compared to a stock module. The reason is the MSD unit will take more time to do it's processing over a regular ignition module. Check timing and report back what you find.