So I just spent an 2 hours logging clips from some documentary footage and now when I go to batch capture I get an error telling me that "You are about to capture drop-frame media to a non drop-frame clip." Is the fact that I recorded my footage using the "frame mode" on the GL2 causing this error? Are there any special Final cut system or capture settings I should change in order to capture frame mode footage?

I get an error telling me that "You are about to capture drop-frame media to a non drop-frame clip." Is the fact that I recorded my footage using the "frame mode" on the GL2 causing this error?
No, this is a timecode issue. You should be able to change the offline clips' settings to use drop-frame timecode from the browser and then batch capture.

IIRC, the way to do this (I'm not at my FCP machine, otherwise I would try this myself first) is in the FCP browser, select all the offline clips and then right-click over one of the fields displaying timecode (for example, in the length column... not on the column header, but inside the actual column over one of the entered values). A contextual menu will appear giving you the option to change the type of timecode. This change should, again IIRC, apply to all selected offline clips.

Awesome! Thanks Mike! I knew it had to be some sort of contextual menu somewhere but google searches came up with nothing and aimlessly clicking through all the menus I could think of in Final Cut left me without a solution. Of course it turns out I was just right-clicking in the wrong spot! :)
Thanks for your help!