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Mike:
The heavy red lead from the MSD box should be connected directly to the post that the (+) pole of the battery connects to at the starter solenoid. The black heavy wire from MSD box directly to chassis ground. You can shorten the leads from the MSD box to the distributor. Is your fan run through a relay (it should), or with a switch. Remove any other electrical items that are on the same circuits as the fan. Be sure you have a ground cable from block to chassis.
The fan and the MSD should not influence each other.
Rick
__________________
Rick
As you slide down the Banister of Life, may the splinters never be pointing the wrong way 
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