Jeff read through this:
http://en.wikipedia.org/wiki/Electromagnetic_Interference
"EMI or RFI may be broadly categorized into two types; narrowband and broadband. Narrowband interference usually arises from intentional transmissions such as radio and TV stations, pager transmitters, cell phones, etc. Broadband interference usually comes from incidental radio frequency emitters. These include electric power transmission lines, electric motors, thermostats, bug zappers, etc. Anywhere electrical power is being turned off and on rapidly is a potential source.
My thought is, if it is happening now, maybe you've moved your plug wires around (bumped) and now they are causing the issue.
When you cut the harness did you move anything else?