iTunes

I'm problems with iTunes as it seems alot of people are according to all the posts. I recently had to reset my Ipod to the factory settings. I had over 1,100 songs on it. When I plugged the Ipod back in to my desktop to sync it, I only got about 500 songs and ended up with lots of explanation points beside my music. If you click on the song I get a message saying the file can not be found and asks if I want to manually find it. That brings up a 1,000 files that have no recognizable path. The music is still listed in itunes, but I'm unable to listen to it or reinstall it to the Ipod. I tried to contact iTunes which got me no where. I have the ability to bring up a back-up, but not sure how iTunes will respond to that. I'm missing music I downloaded from iTunes as well as from CDs.