I had the same exact thing happen to me. I also had a complete MSD system. I tried all of the above. I even replaced the box! The lesson I learned was when you start changing parts, start with the cheeper stuff and work up. The only thing I hadn't changed was the coil. Once I did, everything was back to normal. I will bet that is the culprit!
If that turns out to be okay, it is still good to have an extra lying around.