What happened to half of my music when I switched from iPod to iPhone?

I bought an iPhone 5s back on Halloween, and when I synced my iPhone with my Apple account, it transferred my music over. I have just now realized that over half of the songs and albums that were on my iPod are not on my iPhone. I've checked iTunes on my computer as well, but the missing songs weren't in my music library. I even went into iTunes and looked up an old album I had on my iPod, and only half the songs were listed as "purchased". They wanted my to buy the rest. Everything on my iPod has been reset by my sister so she could use it.

I definitely don't plan on paying $200+ again for music that I've already payed for. What should I do? Any ideas?

Thanks.

Added (1). Yeah but that's the problem, everything I've ever bought IS NOT in the purchased section in iTunes.

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