Norton,
Here are the measurements; The E6 car bodies were lowered to 1 and 1/16th inches over the rail. Due to the anticlimber lip of 1/16th inch or so, the pilot is 1 inch over the rail where it meets the anti climber. The bottom of the pilot will be a scale 4 to 6 inches over the rail. Adjust lowering the Mth body to yield this result with whatever pilot you use.
Be advised I had to bend the cast Lionel pilots to configure to the anticlimber.
On the Lionels, rather than cutting the body posts only, I ground the height lugs on the trucks and trimmed the body posts.
So, it is a little involved. Hope this helps. any other questions you have, just post em.