You must have Win 98 first edition, right? I'm pretty sure Win 98SE (Second Edition) came with IE 5.
In my opinion, you'd been better off not to download the "critical" updates for Win 98; I do the Windows updates thing with Win XP, but I've had negative results with Win 98, just as you have. As you said, now your computer runs much slower. If you want to get it back to it's former speed, you may need to format your hard drive and freshly install Win 98. If you do that, and if you use the computer on the Internet, I would get a router so that you have some hardware firewall protection, and also install a software firewall. And, of course, keep anti-virus software current and use some spyware removal tools to keep it clean.
If you downloaded - download only, not install - Internet Explorer 6 Service Pack 1 on your other computer, could you burn it to a CD, then install it on your Win 98 computer from the CD? If you can't burn CD's, maybe you could ask someone you know to do this. You can clso order a
CD from Microsoft with Internet Explorer 6 Service Pack 1. The cost is $5 plus tax to US residents.