Some ploblems about PCI core

Enabling PCI I/O enables the clamping diodes in the I/O cell.

Be careful though as Cyclone 2 is not 5V tolerant - you will have to use some sort of level shifter between the FPGA and PCI edge connector. Therefore you probably wouldn't necessarily need the clamping diodes enabled on the FPGA

Cyclone 2 will drive 5V logic from its 3.3V I/O but most of the PCI signals are bi-directional so you will need level shifters for the majority of the signals.

You will need to set tco, tsu, th and tpd constraints when you compile the design. If these aren't met then you will get problems on your card.

The PCI spec is quite specific on trace length of the signals so be careful when you lay out your board.