I'd agree; that's a good 1st step for troubleshooting.
1st goal is to determine whether the interference is getting in the EC2 through the power line, the ground line, or it's RF energy entering the EC2 directly, through either the case or the many input/output wires of the EC2.
Someone posted that Tracy had added filtering inside the EC2 at some point. I don't know how he implemented the filtering, but if each controller has its own filters, then one could be missing, or failed.
"I believe I bucked my last rivet last night on the forward upper deck. The plane will be heading to the airport in a couple weeks but will be making a detour to the paint shop on the way. You will like this, when I completed the wiring I ran the engine one more time to verify the newly completed system. To my amazement everything worked, even the interior lights, until I hit the PTT to see if I could pick anybody up. When I pushed the PTT the engine would almost quite and the EM2 would start to scramble, even the FM radio on the garage wall would quite. After a calls to the Gulf Coast Avionics techs is was soon apparent that they led me on a trouble shooting trip that led to nowhere. After a weeks vacation from work and the plane I came home with a fresh mind and discovered a direct short to ground from the coax center conductor to the radio case. A bad radio right out of the box".
It's pretty unlikely you'd have exactly the same failure that Sam had in that post, but you can have a similar issue *outside* the radio. Prep of the coax, or any of the connectors, could result in either RF radiating off the shield (if the shield is 'floating' at either end), or RF radiating directly into the airframe, as described in the text above.
When troubleshooting, you usually want to change one thing at a time. But a variation in troubleshooting (when possible) is to split the possible causes into big segments, and eliminate a segment from the equation. In your case, you could power the EC2 from a separate source, as Jeff mentioned. If so, remember that you likely have lots of grounded devices related to the EC2, still connected to the airframe (leaving a path for interference). You could also borrow another radio *and antenna, with coax*. Wire power & ground direct to the battery, and transmit with nothing related to the original radio operational. If the problem disappears, you know the problem is probably in either your radio or your wiring. A quick check of antenna/coax is to substitute a known-good piece of coax and antenna (antenna can be just hung out the door for this test).
I realize that setting up another radio might be tough to do unless there's a ready supply of spare radios, so another technique would be to use a handheld. Crank the engine, and place the handheld's antenna near the EC2 wiring harness while transmitting. If the EC2 goes nuts, you probably have filtering issues in the EC2.
The above isn't presented in a very orderly fashion; more a 'stream of consciousness' line of thought. When you begin troubleshooting, you need a specific plan of action, with steps written out and checked off as you make changes. It's very easy (I can testify) to get lost in the procedures, and forget what you've changed.
Charlie
electronics tech in a couple of other lives