Sounds like you're going to look at the data the right way. I completely agree there's a lot to look at and that you have to look beyond the simple CTR and CPC. Do you have your AdWords account connected to your Analytics account (assuming you have an Analytics account) or at least do you have AdWords set up to show you which keywords result in a sale?
I'm thinking this won't apply to you, but is it possible there are seasonal trends with certain keywords so you could group them in a way allowing you to turn them on and off seasonally.
If you haven't already done this (I think you may have) it's a good idea to group your keywords into themes and then build campaigns around each theme. That way you can better target the ads to the keywords. Also do you test ads against each other? Are you running more than one ad per keyword group?
The main thing you probably want to do now is tie in the keywords to the actual revenue the keyword brings in. That should tell you which keywords are most profitable and which you either need to drop or change something to improve their profitability.
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