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computer slowed way down

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Two weeks ago after my kids were on webkins in the morning I noticed the computer went into chdisk. After it was done the system stated there were corrupted files. I tried to reboot but the computer stated the operating system was not intact and could not start. I tried a repair from the system disk that came from the manufacturer but it could not repair or boot from the cd rom because it didn't find an operating system. I thought about a new sector boot but the instruction from the cd rom said to do a new install but when I tried that it started areformat and i didn't want to lose my files. I aborted the install pretty quickly then tried a repair in safe mode since it wouldn't boot into safe mode either. The repair didn't work in safe mode but when I tried it in the regular mode again it found an operating system- probably the aborted load. This time it did repair and I could get the operating system to reboot. I copied my files and have been trying to fix the computer since. The main symptom is that it is really slow and won't in fact run some programs because it takes too long and they fail. I followed the trojan, virus instructions and had both malware and avast hang up and not be able to finish. After I ran Rooter I was able to finish the scans but can't repair or quarantine anything found. Malware took 2 1/2 hours but found nothing. Avast listed 2 files but not as infected just problems. I moved all music and pictures off the c drive to the d drive too make sure it wan't a memory issue. What is my next step?
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