If your computer can handle it the best software to do what you want would
be to upgrade to XP. Almost any PIII or better with 256mbs of RAM can handle
it.
In truth no software is very good at fixing registry problems.
Hardware conflicts are actually rare if your bios is set up to allow Windows
to assign resources. When USB 1 was new there were often conflicts if the
USB ports were assigned to share IRQs with other devices, particularly
network cards. This just does not occur with XP and more modern motherboards
but could be an issue for you.
I do not know if anti-spyware and anti-malware programs are compatible with
Win98 but you may have acquired some of these nasties.
Lastly, if your computer is slowing, Win 98 must be manually defragged and
you must look through all the garf that loads at boot up and delete what you
do not need.
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