take the overclock off, and they will never know...
try and seat it better in the slot, and yes, mine has some half-length connectors as well. is there a power plug in the back of it that you are maybe forgetting to plug in?
the PCI bus shouldnt affect the PCI-E bus IRQ wise at all. It should be fine. The buses are separate.
i think you should definatly get a new PSU though.