Goin' with the Bad Drive gang, too. If you get lucky, you might be able to clone your old drive using a notebook to desktop drive adapter kit (about $12-15 at most computer stores), but I wouldn't bet much on it. Still, Norton Ghost or a Pre-Symantec Drive Image might work. You have a better shot at getting your data copied, though I just don't know of a reliable way to transfer your software. Some publishers will replace lost disks, others will just want to sell you the newest version. Check with support for the products in question.

I doubt the mainboard is bad. Problems with failing drive electronics will produce all the symptoms with slow boot, etc. you've described. On the warranty front, you might check with the drive manufacturer and see if you can't just warranty the drive directly through them. I have done tons of work on Vaio's that were still in warranty, but the customers couldn't deal with Sony's slow turn-around times, bonehead support, or whatever, and preferred to pay instead. Even if you have to buy a drive, they don't cost much, and I think you can handle the installation yourself.