BleepingComputer.com: System Restore Issues

My PC has recently had problems booting up (Windows Vista Home Premium with Service Pack 1 starts to load and then locks up - forcing me to switch off the computer manually - something I do not like doing). 5 days ago I found that my pc would not boot up fully, so I retried in safe mode. The pc offered me the option to restore from an earlier version. I did so and now I find that:

1. I have a number of files that are duplicated (one having a number assigned to it, one not). I presume that these are the old restored files. How can I get rid of them or am I forced to live with them forever?

2. Every time the pc boots up (which it now does with no problems) it gives me a message that Microsoft Intellipoint has a problem and asks me to confirm that the program can be closed. Which I do. But my mouse (Microsoft Comfort Optical Mouse 1000) works fine, and I see that there are two versions of this program file, one being numbered, the other not. So what is causing this message? The existence of 2 files, or something else? Why does my mouse still work? How do I stop the message appearing?

3. I am unable to trace my .pfc file on AOL Desktop for the e-mails saved to computer element. When I click on this the folder shows only the e-mails over the past 4 days. I have searched for any .pfc file on my hard drive and come up with no results. Have I lost this file forever? The system restore option said that it would not affect personal files, such as e-mails, documents or folders. Has it just lost the path to my previous file? How can I check this?

I need some input here, and would be pleased to receive anyones clarification/advice/solutions?