Well I have bled it a few times while making sure it was topped up so I dont believe any air got in, the hand brake has pressure but not a lot feels spongy and the rear will go threw the floor befor it will grab which puzzles me because befor putting in the new pads both the hand and foot had lots of pressure.

 

Yes I would agree it doesn't make sense. When you put in new pads with a lot more meat it should make the "pedal" better if anything. Is it possible that some air got in earlier? If air gets into the master cylinder in can be a little harder to get out. Your original post says you had no pedal. Was it the same before the pads were put in?

 

I did have pedal befor I did the pads, now that I think about it the piston was fully extended due to lack of pad so im guessing thats how air may have got in.