if you have the chance, you could load all 5D-footage into Scratch, generate TC and Reel-IDs for each one and export them as ProRes for editing in FCP,
so conforming via XML would most likely give you no problems.
Without doing so, I guess you can relink most of the clips properly through Clip-name and TC (which would be more an "Offset" from start of the clip, than real TC) with a XML from FCP.
If the editing part is -really- done and no further (or at least major) changes are planned, the editors coudl render out a ProRes-sequence with handles and still give you an EDL or XML and you could use the "Reverse Assemble"-function inside Scratch to get each cut and dissolve back.
Delivery-format depends on what the end-customer needs - I'd ask them for specs.
For most web-stuff, I would say QT H264 is sufficient, but it depends.
At least, I'd render out one uncompressed sequence (dpx with seperate BWF-Audio file, or Quicktime uncompressed with PCM audio, if the feature is not too long) for archiving, from which you can convert into different other formats.