Want to restore to factory settings but update to Lion as well

Hi techies....can you help me?

My 2009 MacBook pro is still great but is starting a to chug along a little bit.

I want to restore to factory settings (I have the disks) and would then like to upgrade to Mountain Lion.

Problem is I purchased Lion through the App Store when it came out and I now get an error message when I try to restore to factor settings with my install the disks because my OS is newer than the one of the disk.

Part II of my question is this....I backed everything up on my time machine today so does that mean if I restore to factory settings and upgrade to a new OS that I'll still be able to access all of my old files from time machine?