Not as bad as you might think....
Hey Cameron, I don't think you have too much to worry about. It's VERY unlikey that a Trojan will do this kind of thing to your machine and not leave any lasting effects.
You're right, the problems you're having could well be to do with your sound drivers (or any other driver for that matter). On the other hand they could be due to other things too....
Firstly (and bare with me on this one), do you have any radio transmitting devices near your PC? For instance some kind of walkie talkie or old mobiles are prime culprits for this. Also check that your mouse cable isn't damaged in any way or if you have a mouse extension cable, take it off for a while & see if the problem goes away. I've worked in IT Support for a long time now and have seen this kind of thing happen quite a lot in the past!
Secondly, update ALL you system drivers to the most recent you can find. If you suspect it may be specifically due to your soundcard, remove all sound devices from device manager then reboot and allow the machine to add the devices back. Check that you don't have any IRQs being shared by devices that don't get on too well. If you do, the reinstall the drivers for them. If you know how to change your BIOS IRQ assignments, that is a good way to stop some of the sharing you may have.
Good luck!