Shutdown problems(with 98 espcially) normally had something to do with the network setting. Perhaps you could try to reinstall your network stuff, or disable it. Though...I know my comp with XP just recently seemed to take longer to shut down, and I've not installed anything that runs the the background or change any settings... My lappy with 2000 is still fine... XP just sucks ;P
As for the noise, is it actually louder, or simply just thinking more? If it's getting louder, that's a sign of a dying drive. YOu could check in your BIOS to see if you have a SMART option for the drive. If that's not enabled, try it, and see if it'll catch any problems. Also, being Maxtor, get a copy of their diag disk and run the tests(if you call their support, they want you to do so...)
One more thing, I suggest, if that drive is bad, to get a new one then sell it! I've had SOOOOOOOO many problems with Maxtor drives, I refuse to use them any more. Seagate is the way to go for stability, and that's what my 2 main systems have in them and they've been perfect. Then again, I have a Maxtor drive from the early 90s that still works.