I'm not a PC pro but I know I suffered from some major lag before and I got it to reduce a little by downloading a modified EXE. It's like a no-CD crack and it sounds illegal, but I don't really think it is. I mean, it requires you to have GTA installed (you can't play without the GTA files). I only downloaded the modified EXE for myself because my disk was scratched to shit.
But I mean, if your hard drive is faster than your disk drive, I would recommend losing the disk. Might help.