Something I just thought of, the extra .400" the McLeod flywheel has over stock is actually intended to place the clutch assembly in a factory location similar to how it was in the original application. Now I think there's usually enough adjustment in the clutch arm, but I honestly don't know.
Of all the parts you have now, if you're comfortable with those, the .400 thicker flywheel may be the answer. That would also explain the original suspicions of the arm not being adjusted correctly when you think about it (if the pressure plate and disc are too far forward for the arm to accurately engage it). The .400 thicker would push it back into correct alignment.