Programs Not Opening After Deleting Folder in AppData

Windows 7 Home Premium, Service Pack 1, 64-bit
AMD Phenom II X6 1100T Processor, 3.30 GHz
4GB RAM
AMD Radeon HD 6800


Mine is seemingly a story of blunders. Yesterday I noticed malware called Conduit on my computer, specifically BackgroundContainer.dll (AppData/Local/ Conduit/BackgroundContainer/BackgroundContainer.dll). I quickly googled it, learned it was no good and, in my haste, deleted the entire Conduit folder (and, yes, removed it from the Recycle Bin as well). Then I went to Task Scheduler to remove the error from appearing at startup. While I was in Task Scheduler I thought I might as well clean up my startup while I'm at it and deleted a few other things. Unfortunately I can't remember exactly what I removed but it was stuff that didn't seem important, e.g. Java and Adobe update notifiers etc.

I can't say which of the above actions caused my problem or if I'm at the mercy of some virus but after said actions I soon realized that many programs would not open, most displaying an error. Steam gets stuck in an update loop, iTunes says it 'can't start because GNSDK_DSP.DLL is missing', MSIAfterburner says 'Failed to initialize display driver wrapper', Nestopia says 'found no valid display adapter' (most of my other emulators also give errors involving video plugins and the like). None of this has ever happened before. I've tried reinstalling many of these programs only to be met with the same errors. Booting Windows in Safe Mode yields the same results. On the other hand many programs seem to work just fine, e.g. all internet browsers, uTorrent, Photoshop, Sony Vegas. What could be the cause of this? Should I not have deleted the Conduit folder in AppData? Could removing something in Task Scheduler cause this?

I've scanned for viruses with Avast and removed any infected files, I've run AdwCleaner to remove any junkware etc. (notably some files associated with Conduit came up), I've booted Last Known Good Configuration, booted in Safe Mode, I've run System File Checker ('Windows Research Protection did not find any integrity violations'). No luck. Unfortunately I do not have any System Restore points.

Please help. What could be the problem here?
 
I have win/7 pro, 64bit and iTunes runs
but GNSDK_DSP.DLL: Not found in AppData :)

AppData is (duh) for the applications. Deleting a folder within AppData should be fatal TO THAT application and that one only.

It is true that any EXE in AppData\* ... is suspect - - the app was not installed as an Admin OR it's a virus.

I do find several DLL files within AppData\* ... so these should be expected.

Uninstall and Rinstall of a failing application should resolve that app.

*Conduit* itself should be blamed for your existing issues.
 
The fact that you just deleted it may have caused to the applications to not work correctly, so a reinstallation should of those failing should resolve the issue.
 
Ran some more AV scans, got rid of some infected files. Reinstalling fixed a lot of programs but some seemed to be having DirectX issues. Reinstalled DirectX and my GPU drivers and everything seems to be better now (let's hope).

Thanks for the assistance.
 
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