I'm not familiar with the MSD distributor that also has a module and not just a pickup coil. But, if you have the polarity of the pickup coil reversed it can give you a strange misfire that doesn't necessarily show up until higher rpm. On my dyno I have a switch to flip the polarity of the MSD ignition pickup while the engine is running. I run it and watch with a timing light and in my case I always use the more advanced setting:
Taken from MSD's website:
If youre not sure about the polarity of the pickup you are using, there is a simple test you can perform by checking the engines timing. Check the timing with the pickup wires connected one way, then swap the wires and check the timing again.You will notice that the timing changes significantly and may appear very erratic. The correct connection depends on the ignition control that is being used.
Analog: If you are using an analog controlled MSD Ignition such as a 6A, 6T or 6AL series, SCI series, 7AL series, MSD 8 or 10 or Blaster Ignition, the correct connection is when the timing is retarded.
Digital: When using an MSD Digital-6 or Digital-7 Plus, or the Programmable Digital-7 Ignition Controls, the correct connection is when the timing is more advanced.
Is it possible that the pickup inside of the distributor could have had the leads reversed when you swapped out the module?