odd clutch problem???

I have a 98 GSX and i just rebuilt the motor and put new clutch in, etc.. When i am driving in town and using the clutch or even when i engage the clutch within a half hour, everything works fine, but when i go for more than a half hour without using it, when i go to use it, the pedal goes all the way to the floor and then i pump it a couple of times and it works just fine again. Anyone have any ideas on what my problem is? And does anyone know how to "break in" a new motor, i heard somewhere that what the owner's manual says is about the worst thing you could do... Let me know. Thanks.

ithink to break in a new motor, you cant engage in high speeds for at least 500 miles. and you should check so of the seals/bolts around your tranny for any leakage and maybe it just needs to be re-bled. Just some thoughts.....

bleed the clucth better make sure you get out all the air bubbles.

check the master cylinder for leaks, also inside the firewall where the pedal connects to the cylinder.

Yes, Inside the firewall si where you check for master cylinder leaks. To check for slave cylinder leaks, pull back the rubber boot and look for fluid.