Someone on the Apple support gave me an answer that actually works. Here is what I did.
I jumped back into Premiere and noted the time code in points for each of the clips, then I hopped back into FCP and selected a clip in the browser. Then I went up to the modify menu and selected timecode, then I entered the time code recorded in Premiere. I just did that for each clip and it worked just fine.
Now I just have to get my Sony deck to work with FCP so I can capture directly.