My CD drive was not appearing in the My Computer window so I ran the regedit and deleted all of the upper and lower filters...now my keyboard and mouse will not work. The computer boots to the desktop and the mouse arrow is there but does not respond. Not too sure what to do.

if you didn't backup registry before making the changes to it ,then i suggest a system restore back to the day before you edited the registry .

instruction here .http://tinyurl.com/ykgps6

The only problem is that I cannot use the keyboard or mouse to access the start menu. I have tried unplugging and replugging them, turning off and back on with them unplugged, and just about every combination therein. Silly question but would using a different keyboard and mouse help? Another silly question, I've heard of starting in safe mode...how do I do that? and would it even help?

it sure wouldn't hurt to try another keyboard .what type of keyboard and mouse is it USB or PS2
you get to safe mode by hitting the f8 key, will only work for you if the keyboard works before windows is started ,