Looking at Marks picture, there are unshielded wires going to the fuel injectors which are routed in the vincinity of the alternator (less than 10inches). That Could very well be that.
Try a quick and dirty shielding with kitchen aluminum foils, wrapped around the fuel line and the wires and test run on the ground. If it works, then do a proper aviation-grade shielding.
Philippe CHENEVIER



  Hello Paul-

  We got a free lesson in electromagnetics today.  After I emailed yesterday,
  we went to run the engine again & it ran terrible!  Terry had diddled with
  some of the computer settings, so we thought perhaps we'd screwed something
  up.  We reviewed the settings & discoverered the EC2 tach setting was way
  off -- 572 vs the not-to-be-changed value of 515.  Terry fired up again &
  all seemed well.

  Until... I noticed the EM2 reporting continually decreasing line voltages...

  I looked at the switch panel, and saw we had the externally-regulated
  alternator off-line.  I flicked it back online... and... disaster.  Suddenly
  the engine was trying desperately to stop & could not be adjusted to run
  smoothly.  Flicking the alternator off resulted in fairly smooth running.
  Every time the alternator was brought on line, the engine went bananas.  As
  soon as it went off line, the engine became much smoother.

  Here's a test for the group:  Why is this happening?  Here's an old
  photo
  which pinpoints the problem for those with sharp eyes...

  Mark (Rocky Mtn High)



  Could it be that you have a steel braided fuel supply cable in close proximity to the alternator?
  John




Looking at Marks picture, there are unshielded wires going to the fuel injectors which are routed in the vincinity of the alternator (less than 10inches). That Could very well be that.
Try a quick and dirty shielding with kitchen aluminum foils, wrapped around the fuel line and the wires and test run on the ground. If it works, then do a proper aviation-grade shielding.
Philippe CHENEVIER