(II) Primary Device is: ISA
Your X server is very confused about which device is primary. Please uncomment the BusID line you have in xorg.conf and generate a new log. Please also attach the log from the vesa driver.
Typically the X server will do a PCI bus scan and list all of the devices it finds right before the line that reads "(II) System resource ranges:". It looks like your X server didn't do that. I'm not sure what could cause that problem, but it sounds like a bug in your X server or kernel. Could your X server have been built without PCI support somehow?