Re: New install after virus, hardware issues.
Your HDD is most likely dying, the grinding noise tells me that much, even though it has stopped for the time being.
Can you boot into a 10.04+ Live CD and check it's health via Disk Utility, assuming it supports S.M.A.R.T.
You also might as well replace the CMOS battery, as you had to remove it originally to get it to boot. I bet it either A. Has a Weak Charge, or B. Is dead.
I highly doubt it was a virus, I haven't run into one yet on any Linux OS.
Xubuntu 10.04.2 Lucid Lynx AMD64 + Xubuntu 11.04 Natty Narwhal Alpha 2 i386+PAE (Used for maintaining my Grub2 EFI bootloader), Arch Linux AMD64.