I'm running an MSD 6A without any problems.
I've heard that the multiple sparks can help with emissions........
What gap are you running on the plugs? You can go larger with the MSD (.044)
Also, some low readings with compression are due to the compression tester. The valve is a tire valve, and it takes some pressure to open them. I've had compression gauges read 25lbs low until I found a looser tire valve (hook up to your air compressor to test)