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Advice for getting a machine running better after removing malware

Yes, I realize that the best solution to malware is nuke and pave.

But my perception when there isn't a bare metal image such as ShadowProtect, the process can take several labor hours and is very tedious. Certainly, pop in the dell OS DVD and run that is straightforward. But a long standing gripe of mine is that even when you enter the service tag for a dell computer, their download page lists drivers for all the possible NICs, video cards, et al. My thoughts would be that with the service tag, their site would show just the specific drivers for that exact machine. Am I mistaken? And then install Office, any other apps, Flash, Shockwave and many others, then install updates and restore the data.  But things still  aren't back the way the machine was before

So for cleaning the machine, we through many apps at the machine such as superantivirus, malwarebytes, ADWCleaner, hitmanpro,! hijackthis, eset online and Trend online scanners, autoruns and others.

In the end the machine winds up clean. But may not be running as well as it could. My thinking is that the malware inserts itself in the flow of the data in the machine and removing them still might leave some hooks to the malware and that slows things down? Like LSP entries in older versions of windows?

Would anyone have advice on what you would run to help refresh things after the malware was removed?
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John
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no.  they are saying things are slower now.  I used process explorer and don't see something unusual / no high processor / RAM usage.

Just all things running slow. No rootkits are on the system.
It could need defragmenting  but that is a long shot. Since hardware seems to be normal, I would say rebuilding (steps I noted) are in order. You could otherwise spend your time in a black hole.
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@BeGentleWithMe-INeedHelp  - Thank you and I was happy to help.