Jared: It is the other way around. The first VRI horseshoes were flat. Later on they started bending them to resemble the vintage pickups. It was probably done to increase the clearance so the strings would not hit the bobbin or shoes.
Alan, when the shoes are in contact with the magnetized pole pieces they will appear to be magnetized themselves. The pole pieces you have aren't adjustable, even so they should be pretty close the right arc unless your bridge saddles are filed badly. The "beating" sound is the string too close to the poles. Those pickups have heaps of grunt so I'd back the whole thing off and adjust upward until yer happy.
Yep, that did it. I didn't try this sooner because I didn't think it would have such a noticeable impact.
The response is now much more even across the strings when using the HS alone and the 'phase' effect in the upper registers of the A string is gone. Thanks Gerry and everyone else for the good advice.