Long time reader- first time poster....
Anywho.... I'm essentially doing the same thing. I have about 5000 feet of S16mm at Postworks right now. Its 36 cents a foot to go to HDCAM SR then $150 an hour to put that on to a hard drive. I gave them stock and a hard drive so add $300 and $400, respectively, to the price (plus another $250ish for back up HD). I've asked for 10 bit 4:4:4 uncompressed files. Even if you wanted to down rez to ProRes HQ or any of the other HD codecs, starting with the highest possibly quality digital files will essentially let you work with whatever works best for you.... at least that's my philosophy...
What i plan to do is take the huge (7 GBs a minute) video files and put them through Compressor to make SD copies of the files. I'll probably use ProRes for the codec, but i'll figure that out when I get my stuff back. I'll then take the SD files and cut the short on my MBP using FCP. Once i get to picture lock, I'll go back to full rez files for color correction and my one effects shot. I am lucky enough to have a friend with an HD capable rig, but even then, once i get to picture lock, real-time editing isn't all that necessary.
I'll be finishing on Blu-ray or DVD (I hear a rumor that you can burn 20ish minutes of Blu-ray quality video on a standard DVD-R) for cast and crew then eventually go back to HDCAM SR.
....but to answer the original question... Codecs? Shmodecs. Uncompressed is the way to go.