I had (have) the same problem. Remove the brake pads and taper them using emery cloth. The taper should be wider at the entry part of the brake pad.
Looking from the brake caliper side the rotor rotates upward or into the lower part of the brake caliper. This part of the brake pads should be wider or thinner tan the other end of the brake pads.
I learned this when I installed a 320mm brake rotor and it howled terribly. The neighbors had a new baby so I removed the rotor. The EBC brake pads are supposedly very good though do have a history of squeeling or howling. My rear barke occasionally howls.
another answer is to get a softer brake pad though it will wear faster and might stop less efficiently.
2005 KLR 685
2015 Yamaha Super Tenere ES, 5/23/2015
2012 Yamaha Super Tenere; Purchased 7/30/2011; Sold 5/23/2015