Replying to Big Itunes Trouble- HELP!

My hard drive crashed but I still had all my music on my ipod. I downloaded this program to rip the music from my pod to the new HD before I realized I could do it manually. I used the program and now 95% of my music is fucked. The song either skips like crazy and restarts etc, or the song plays for a little then just ends wether its 30 seconds in or 2:30 in it varies for every song. And some show up but simply don't play. There is nothing visually that sets the bad tracks apart from the ones that work. They appear fine and it shows their full length on my ipod but they either only play for a little or not at all. I don't even enjoy my music anymore, I just get soooo pissed as it skips through 25 sound clips instead of playing a song. Any advice at all? I think I'm going to have to erase it all and start from scratch which sucks cause I have so many underground rap songs/mixtapes that I have no idea where I got em but I love em. HELP ME NS! Thanks