The Possible After Effects of a Virus

I'm new to this forum and I apologize if this post is too long, if I don't know how to properly describe the specific details of my isssue or if this is the wrong thread (I assumed it was a malware effcted issue)...

I'm running Windows 7 64-bit, on a Toshiba Satellite L555, Pentuim Dual-Core, 4GB

A year ago I had a virus that I thought I successfully removed by following the removal processes in this forum (I hadn't joined yet), running each program in the order advised and so forth. The effects of the virus seemed to be eliminated. About 3 months later I discovered that files in my registry had been completely removed and never replaced after the virus removal and I followed Microsoft website instructions on how to replace the missing files.

Everything on my PC was working fine and had been until last month. My laptop began taking an extremely long time to reboot, like 15 to 30 min of being stuck on the windows icon screen, another 10 min after I logged in, then it would run fine after it finally restarted.

I had my computer looked at, scanned, and cleaned by someone else this time, I didn't go through the Major Geeks malware removal process. When a system restore was a attempted thinking that it could've possibly been an update causing the issue it was discovered my system restore had been disabled and when re-enabled there were no restore dates available. I assumed that when I had removed the virus last year that this was a configuration I hadn't changed back afterwards, although I couldn't remember really. When the guy I had look at it wasn't able to figure out the reason it rebooted so slow he ended up doing a full system restore to the way it was when I bought it.

This seemed to do the trick until this past week or so. Now it doesn't take as long to reboot, but after a restart everything runs really slow, there time delays in clicks, opening applications, typing, scrolling, ejecting devices ect. So if I'm attempting to install, uninstall or immediately get to work on something it take a long time to get tasks accomplished. Then after it's been running for 15 - 20 min or more everything seems to run smoothly with the occasional delay, which is actually happening as I'm typing this, my typing is delayed. However, web browsing isn't really slow at all (I use firefox).

Are these delayed after affects of a virus, proof of an existing virus, some issue with windows software, or signs of bad/failing drives or drivers?

Thanks in advance for taking the time to read all of this.