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may be u can get help from xilinx,altera..(or company who are making IP's for PCI...
u can dwnld their datasheet...and make a list of checklist/different cycle to checks..
after that u can use any ready made schematic of PLX with FPGA..
and from the local side of PLX u can debug the PCI bus...
on one side of FPGA there will be local bus of PLX and on other side serial port for connecting PC or JTAG