What height are the strings from the poles? May sound a bit counter intuitive but to get an even magnetic flux with these it's sometimes better for the pickup to be lowered.
As a point of reference, I have a '57 P (single coil) with flat poles and get a good string balance with the following setup (measurements in inches):
G - 12/64
D - 16/64
A - 16/64
E - 13/64
I know the stacked pickup is taller than the regular single coil which might possibly be part of the problem. Close pickup settings will accentuate the G and E, but set them up with a bit of air and they produce a wonderfully rich piano-like tone. Beautiful things!