To be honest I would leave the pads, if the brake isn't making a squealing noise they should be fine.
Disc brakes work on a totally different principle to rim brakes, everything needs to be flat, smooth and free from contaminants (oil, tar, dirt, even the oils in your skin will reduce brake performance!).
My advice would be to check the set up again - pads hitting squarely, at the same time, no rubbing etc - then go outside with some cold, clean water and chuck some on the rotors. Scrub the brakes on and off lightly and you will probably start to see black gunk dripping off the rotors. Clean this off (loo roll works great), apply more water, and repeat until the water stays clear. That should clean them up nicely
Very difficult to diagnose stuff like this without the bike, but give that a go and things should improve...