It depends on what hubs your gong to use, It might not change the "rotor offset" at all which means it will still sit off to one side in the caliper, and with the other problem i dont think you'll solve that either, the cailper will still be bolted onto the same part of the hub houlsing arrangment.
I would machine the overall diameter of the rotor down to clear the inside of the caliper, and depending on what way the caliper needs to move to center the rotor either machine material off, or make a spacer.
Hope this helps, do you have any pics??