I don't think I can help you if you are missing a large number of songs as, at least with they way I fixed mine, it would be quite obvious what is wrong if it happened to 100 songs. Anyway... The problem I had is that if you have 2 of the exact same Files the iPod will only take one of those.
What I did is put my iPod on manual, made 2 smart playlist by kind in both my iTunes library and iPod. one was for Files containing AAC and the other for containing MPEG. I checked to see what the difference was in the one I made in my Library and the one I made on my iPod. For example in my AAC my iPod had two less then my Library so I sorted them by name in both, put the windows side by side and went through until I found out where the numbers got off and I found that they were duplicate files in my library so I deleted one of those files. I repeated this in my MPEG smart playlist. This could be done by comparing your iTunes library to your iPod Library as well, I just did it this way because with a smaller list in makes it easier to find the files that are duplicated
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