No, you didn't screw up.
After you do an "over the top install" as you have done its not unusual to have to reinstall some programs. That is at least partly the case here.
Cannot find C:\WINDOWS\SYSTEM\regsvr32.exe
Go to Start>Run, type in msconfig and look under the Startup tab to find the associated program. You can uncheck it to stop from running at startup or reinstall.
"ksclockf.ax","ksdata.ax","ksinterf.ax", "ksvpintf.ax", "ksuser.dll","
Those are all associated with a webcam? You may need to reinstall the cam or stop it from running at startup.
cwbaudio.bin and cwbase.sys are associated with a sound card. Go to Start>Settings>Control Panel>System and look for any yellow exclamation marks or yellow question marks and let us know what they are. You can get those two files from the 98 CD by going to SFC and using Extract. You need to know where they go. After you extract them, check System again to see if anything changed.
When the only tool you own is a hammer, every problem begins to resemble a nail. Abraham Maslo
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Trying to remove your data from the web is like trying to remove pee from a swimming pool