Hey James,
I don't know if it's any faster for you but you could try Mpeg Streamclip for your transcoding. Any chance of upgrading to FCP X, you should be able to work natively there. I use Adobe Premiere Pro and work in native file formats, it's pretty nice to go straight to work compared to when I had to transcode everying in FCP 6.
I have a D7000 and you're right, transcoding is a must if you plan to use Final Cut 6 or 7. Your only choices are transcode, or use a different editing program.
I've only done one project with the D7000, I set up a batch convert with MPEG Streamclip and let it work.
Thanks James and Peter,
I turn my 5DMK2 files in to Apple Prores 422 (LT). It's a pain to have to wait for it to transcode but that's just part of the process. If you shot tape you would have to wait for it to ingest.
My newspaper just picked up a D7000 to shoot video with and after pouring over various forums, I'm learning that it shoots in H.264, a compressed video format that doesn't play nicely with Final Cut Pro... especially if you are mixing with other uncompressed files shot from other cameras.