+1 for bleeding the brake lines... sounds like you have an air bubble in there... or some water in the fluid... a good flush will greatly improve your braking.
Also, good advice on giving them a bit of time... new brakes need to have a break-in period where they score and match the imperfections of YOUR rotor before they make good contact with the WHOLE surface of the rotor... right now you may only be making 75% contact due to minor ridges and hills... which naturally occur on any rotor.
2002 VT1100C2 Sabre
1985 VT700C Shadow
1999 CB750 NightHawk (son's ride)
"The Hardest Part About a Zombie Apocalypse, Will Be Pretending I'm Not Excited