well... gave it another try today and had no luck. cleaned the piston off until it was nice and shiny and it still drags. the wheel is definitely aligned too. not sure whats causing it to drag.
Did you bed the pads properly? Did you prep the rotor for new pads?
How much of the piston did you clean? Just the portion showing after you pulled the rim off or did you push the pistons out further and clean as much as possible?
Are there any other problems that manifested at the same time?
Sorry for all the questions, but diagnosing an illusive problem via the interweb is challenging!
The fact that the rotor only contacts at select points should be an indication of something spinning out of round. And bear in mind, that aligned with the stock markings on the swingarm do not necessarily mean it's aligned. Ask me how I know that, I'll tell you an expensive way to figure that one out
Google string method tire alignment, there are many ways of aligning it properly but that's what I used after paying someone $150 to look at it when I couldn't get rid of a wobble, and guess what it was.... TIRE ALIGNMENT!
A way to do a check for rotor run-out too is to scribe a line on there with a sharpie or similar (just don't use a grease pen) and spin the tire, where it gets worn off is where there is a potential problem. Make sure there isn't detritus on the back side of the rotor causing it to be raised from the rim.