Spyware and system resources problems

I arrived home the other day to find that I had an entire host of problems on my computer. I ran Spybot and found a large amount of spyware. I eliminated them, but problems persisted. Eventually I discovered that I was still running 1.2, so I promptly downloaded 1.3 and got the updated. I got rid of most of the ones that I hadn't detected earlier, except for Twain-tech, which causes Spybot to freeze every time I try to remove it. I am aware of the guide to removing this in the sticky above, but I can't follow this as I do not seem to have most of the files mentioned in the guide (my only explanation for this is that Spybot may have removed parts of it before it froze). Twain-tech, however, is just a nuisance and a possible cause of my problems. I am experiencing frequent pop-ups, which I believe is being caused by Twain-tech, but I also have a very low amount of system resources, usually with only about 20% free. Obviously something is eating this up, but I don't think Twain-tech is the only one. I fear that the cause may be deeper. Can anybody help? I'm running Windows 98 on a 56k modem. I can provide any other info you need.

PS: Sorry if this is a double post. I posted this earlier (I went more in-depth on that post), but I came back and there was no record that I'd posted.