When you try to shutdown, exactly what does it do? Does it go part way and then hang? 98 was notorious for a shutdown problem to the point that MS issued a patch just for this problem.
You can get some shutdown troubleshooting help at:
http://www.pcpitstop.com/techexpress/shutdown.asp
I would try shutting down your machine however you can and then letting it sit unplugged from the wall for awhile to let any residual charge in components, capacitators etc. discharge. How long? Be extreme and give it a 1/2 hour to be sure. Then plug it back in and try it. Run scandisk again. Good luck