you munged up the specs, so i looked it up:
1 x PCI Express x16 slot, running at x16 (PCIEX16)
1 x PCI Express x16 slot, running at x4 (PCIEX4) (Note 3)
2 x PCI Express x1 slots (The PCIEX1_1 and PCIEX1_2 slots share bandwidth with the PCIEX4 slot.) (Note 3)
(All PCI Express slots conform to the PCI Express 2.0 standard.)
3 x PCI slots
(Note 3) The PCIEX1_1 and PCIEX1_2 slots share bandwidth with the PCIEX4 slot. When PCIEX4 slot is populated with a x4 card, the PCIEX1_1 and PCIEX1_2 slots become unavailable.
It sounds as if you'd be restricted to 4x on the second slot. Also, you should not have anything on the smaller "pci-x 1" slots, because those will not work at all when using slot 1 and 2. unless you added a wifi or tv decoder card to the 1x pci-x slots, then that should not concern you.
No idea how the 4x speed changes the mining behaviour tho. Does mining need a lot of i/o bandwidth? If yes, then you could be restricted by the reduced speed, if not, then go ahead.