You might have used some grease around the pad where it wears on the pad holder/piston. That might have gotten on the discs/rotors. It does take a while for the pads to seat, but until then you normally get some squealing or whistling. The new pads are perfectly smooth, the old discs/rotors are not, the new pad need to "seat." That could mean less braking at first, perhaps, but not by much.
As far as having to push much further now, that has me puzzled. Some systems, when you push the piston back in to fit the new pads in, will actuall expell brake fluid out of the resevoir in the engine compartment. I've never had this happen and my dad is always surprised that I can change my own brakes without have to top off the resevoir afterwards. You might just want to check your DOT fluid, make sure it's not low...i'm not sure if this would lead to having to push the pedal down further than usual.
I have notice that the first couple times after changing the brakes, the pedal goes almost all the ways down to the floor as the system redistributes the DOT fluid and calibrates itself for the thickness of the new pads. But this only happens like the first and second time your step on the pedal after changing the pads.
I'm stumped. I would check the DOT and keep an eye on it as you drive the first 100 miles. If the pedal still has to be pressed really far, something is wrong. You should not have to bleed the brakes after changing pads or discs. Bleeding brakes is only something you do every 3 years or so, just to keep the fluid fresh.
![[rolleyes]](/images/smilies/rolleyes.png "Roll Eyes (Sarcastic) [rolleyes]")