Andrew,
Sounds like you’re dealing with a lot of footage in the multi-clip. My, admittedly untested, idea for using footage from a camera that doesn’t record the whole time, and / or has timecode breaks in multiclip is to set the footage up the old fashioned FCP “multi-clip” way… stack ’em and sync ’em.
With your matching timecode, you may only need to use one other shot on V1 (say a master shot or drop shot) and sync up your roving clips on V2 in the correct places.
Once that’s done, delete the clip from V1, or turn the track off, and export a reference movie. Import the reference movie and use that for your multi-clip editing.
If the performance isn’t there, you could export self-contained… it seems as if you have the disk space. When it comes to recapturing, since it sounds like you won’t stick with DV, you’ll have to go back to the setup sequence, and recapture from that. You’ll probably also have to re-export, and reconnect your multi-clip to that.
I realize that may sound a little sketchy, and there is a hole or two in that workflow, but that might help your load times / crashes.
Zak