Q: iTunes, iPhone and music

I was having difficulties updating iTunes to 11.1.1 so I uninstalled all the apple software off of my laptop and redownloaded it. When I view the music on itunes it shows everything that was there before but wont play the music with exclimation marks. When I disconnect, all of the music with the exclimation marks wont display on my iphone (most of the music that does work was music i bought on itunes). Does anybody know how i can get my old music to work on itunes and how do i get it back onto my iphone? I manually manage music and videos onto my iphone. On itunes it says i have 93 songs but on my iphone i have 13.