The Canon E1 plugin used with Log and Transfer should be able to add time-of-day timecode to the converted H.264 clips.
I would think that, rather than waste time adding times to file names, you can just lay them onto a timeline, sync each angle to itself first, and then combine them. That way you can just do the entire angle offset at one go. Also, that would allow you to check the integrity of the sync.
I would suggest that before you sync, you add a Nick Meyers timecode burn overlay (ie. using a Text object) first, with the burn matching the timeline timecode. That would speed you up very quickly so that when you open a clip, just take its Media In timecode and fly it right to that point in the timeline. That overlay would also allow you to account for the timecode lapses when the cameras weren't rolling.
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