Windows possibly corrupted

OK, my malware issue (which I believe is now fixed) has become something of
a software issue. In a nutshell I think Windows may well be broken, to some
degree, but in what way I really can't be sure.

Issues I have noticed are:

Issue1

My mouse and keyboard will randomly freeze for a couple of seconds
intermittently. I thought this might be related to Spysweeper but after
uninstalling that it is still an issue.

Issue 2

The help and support button off the start menu didn't work. I got a
helpctr.exe couldnt be found message. I did manage to resolve this. I also
got a similar error when trying to run msconfig, which again I managed to
resolve. Key processes seem unable to function properly as Windows almost
literally can't find it's arse from its elbow.

Most frustrating of all is that when I was trying to run winsteng.exe which is
vital to getting an Adobe Postscript driver port set up I got told:

The Win 16 Subsystem was unable to enter Protected Mode, DOSX.EXE must be in
your AUTOEXEC.NT and present in your PATH.

Chaslang gave me advice to run XPproFix and XPHomeFix which seems to have now enabled that program to run. However the fact remains that XP has all these annoying little problems and no doubt tons more I don't even know about. I have run sfc /scannow and it didn't seem to do anything at all.

 

Was that advice on how to get Help and Support to work because you did that before and it got it working. I'm not actually trying to fix that now I'm trying to tackle the wider issue which that was just one symptom of.

 

The wider issue is basically that Windows seems to be damaged. Not severely as it's still running more or less without issue (other than the occasional damn annoying freezes) but it seems to need a hand in finding stuff it should be able to find easily.

I haven't done a repair install, other than running sfc /scannow which seemed to do nothing whatsoever. I'm a bit lost as to how to go about it to be honest. Doesn't it involve hitting F8 in the boot process and doing something from there? Sorry, I am so rusty, I tend to leave well alone if things are working ok and I haven't really messed with this sort of thing for pushing 2 years. It weren't broke so I didnt try and fix anything!