3
ive check your mobo's manual and the 3rd slot (second x16 slot) runs on only x4 speed. in theory you would take a big hit with reduced bandwidth, but considering your ancient gpu, i would guess it should translated to a +-10 fps hit. still a hit but at least it could work.
if your gpu isnt outputting anything, it could means your motherboard is still training to recognise your gpu. power off completely and try again.
plus, i dont think the sata ports get in the way of gpu, firstly they are flat mounted, not facing upwards. secondly it could mean the pch heatsink is getting in the way. the easiest solution is... try another graphics card.