No, the mobo wont beep with no graphics card, its that fact that it beeps with no ram that makes me think its the graphics card rather than the mobo thats at fault.
Are you in the UK? Cos if so i can send you an old pci card to test with!!!!
It's probably the motherboard I had an ASUS board withe same symptoms you have and when I replaced it the system worked fine. although those scrathes are small they look like they are down into the tracks on the PCB which may cause a short. Only one question did you use silver thermal compound? if so makesure it isn't causeing shorts, even a small amount of residue can cause a short(many northbridges have surfice mount resistors which are close to the die and can easily cause a short from excess thermal compound). If it causes a short clean it off with acetone and apply new paste maby non-silver this time.
those buldges do look abnormal. Thermal paste can't be the problem as the white silicone stuff is non-conductive. This leaves your motherboard as the most likely culprate.
Can i use an SLI motherboard with a ATI x800GT graphics card?
As i dont play games i dont really need an SLI motherboard (as i will only use 1 graphics card) but the features seem to be better on these boards for the money.
You can use SLi with one ATI videocard but if you want two video cards you will need to get nVidia cards. I would stiil recomend a motherboard that supports SLI or Crosfire so you'll have that option if you decide to upgrade later and it doesn't cost much more.