Well if you want no installed software (except for a BIOS) then why not build your own...
Q: how do i know the CPU will fit the board?
A: Just make sure you get AMD stuff, they dont change the socket every month. But if its a PIII then get a P-III motherboard.
Q: what RAM will fit my board?
A: If its brand new, then DDR most likly. But your looking at more of a late model P-III, so SDRAM in your case.
Q: what pitfalls and limitations do things have?
A: Lots if its intel (im never buying it again) make sure you dont get an onboard video card.
Q: how many ISA/PCI slots should the board have?
A: If your looking at a late model PIII then it wont have ISA slots! But 6 is enough, maybe 5, my system has onbored Video and sound, so it has 4.
But by the looks of the system your looking for, you could just buy mine...
PIII-850mhz (does seti units in 9 hours), 20gb of hard disk drive, Intel 810 onbored video, AC 97 onboard sound, Advansys SCSI controller, 2 network adapters, 1 IDE CDROM 32x, 1 SCSI Burner 4x, 4 usb, 2 serial, 1 parport, 1 Panasonic 1.44mb FDD, 1 good looking case, 192mb of PC100 SDRAM.