|"what is the performance downgrade because of this?"|
None; the 9400GT is far too slow to saturate a 1.0/1.1 PCIe x16 bus, let alone a 2.0 bus.
"do any of the card specs turn off?"
"whould i nottice difference in a pci express 16x 2.0. inbetween pci and pci express 16x there is a 2.0 in white."
Mind rewording that for us?
Pentium M oc'ed to 2.82GHz, 667FSB, 2MB L2
3GB of DDR-800 @ 667MHz
Modified PowerMac G4 'Quicksilver' case
HDMI to homebuilt 1080p projector