MSD prob

If I had to guess I would say the MSD box is just putting more load on the charging system at idle, which makes it more noticable.
Here's a few good links.
http://www.moparts.com/Tech/Archive/elec/34.html

http://www.moparts.com/Tech/Archive/elec/10.html


http://www.essex1.com/people/rebuild/drop.html

One thing the last article says
"Hint, did you check the bulkhead connector for a hot or burned connection"