I had a similar problem with Shimano hydraulic discs. I went through the same steps as you many times. Cleaning the pads and rotors with alcohol, sanding them slightly with 200 grit sandpaper, etc... The brakes would eventually start howling after a short ride. Examining the brake while applying them on the stand revealed that one of the caliper pistons was not activating as much as the one on the opposite side of the rotor. So, as the 'good' piston pressed up against the rotor, it actually was forcing the rotor towards the other piston, causing lots of pressure and the squeal. I replaced the entire caliper and now have quiet brakes.