Did you ever run the master cylinder low? But it sounds like your symptoms are from pushing the pistons back. I've done the same thing a couple of times. Basically, when I pushed the pistons back to install the new pad, it pushed fluid back through the system into the master cylinder reservoir. Then when you step on the brakes, the system is having to move much more fluid to get the pistons/pads back. Usually this will resolve itself since after enough stops, the pistons are back to normal. Its the same reason that some cars get mushy brakes with BBKs, the new larger caliper needs a lot more fluid than the master cylinder is designed for.
This may be obvious, but you're not low on brake fluid are you? That can also cause similar symptoms. If that's not it and you're 100% sure your brakes are bled properly, just try some hard stops to bed the pads and this should solve the problem. It always did for me. The fact that you have to pump the pedal and it gets firm is exactly what I experienced.
Why did you have to bleed the brakes for a pad change though? Or did you replace brake fluid at the same time?