Just as a point, pad contact area has no effect at all on braking force. Seems counter intuitive, but if it did I'm pretty sure all pads would be a lot bigger. Pad size mainly effects wear rate, and the main benefit of 4/6/8 pot calipers is that they can take a bigger pad which will last longer. If you ever get a chance, have a look at a rear pad for an alfasud. They are about the size of a postage stamp.
For your braking problem, if you have new pads and discs did you give it all a good dousing with brake clean when you'd finished, and then follow the bedding in procedure correctly?