Did you bed them in correctly?
Not sure what that means. But was done at my LBS so I'm assuming the install was all kosher. Did you also change the rotors?
very fine sandpaper
You might need to take very fine sandpaper to the rotors and then clean off with isopropyl alcohol if the disks are glazed. I did this when I changed over from avids to XT
Sram Guides.
To late, once shimanos are on might as well just get a new bike.