Should I cut footage into clips whilst I'm logging it?
There is no right or wrong answer here.  I've done both before for projects of your scale.  There are factors that work in favor of both.

For recording whole tapes while you take notes by hand, the pros are:


Least amount of calendar time to capture and edit.
Technically simple.
Requires detailed viewing and review of footage, which may catch issues earlier. (Note, you still CAN review footage in detail for clip logging, but you also don't have to.)


Cons are:


Requires your attention for the entire length of capture to make sure you don't miss anything.
Doesn't allow for as easy use of DV tapes as a backup mechanism. (You can save the start and stop time for the whole tape, but can't import a single clip.)
Requires manual splitting of clips after, however this operation is fairly quick as you have a listing of time codes on which to split.


Conversely, for batch logging of individually logged clips the pros are:


You can fast forward through tapes to get the clip identification done more quickly that watching all the footage in real time during capture.
Allows you to easily go back and double check a missed transition's time without interfering with capture.
Requires only periodic presence during actual capture.
Since meta data for clips is electronic and based on exact time code, DV tapes function as an additional backup.  Footage can be re-captured in a frame accurate manner in the future.
Clips come out as distinct files with well documented meta data.


Cons of individual logging:


Requires more time overall.  You aren't actually capturing while you are identifying the clips and the extra time you spend up front is generally longer than you would have spent splitting clips after, both due to the seek time for tapes as well as the time to enter electronic meta data instead of simply writing it down during playback.
More complicated technically.  You need to actually fill out the meta data for the files to make most effective use of this logging technique and it is more complicated/time consuming than simply writing it down on a pad of paper.


Overall, it really comes down to how organized you want the data to be and how much time you have.  If you need the project done in the minimum amount of calendar time, capture it all and log as you go.  You can alternately do scene breaks as you go as well.

If you more calendar time, are sure of your captured footage, want some additional long term organization and don't want to have to supervise it attentively for 50+ hours, then use clip logging in advance and batch capture the tapes to fill out the clips.

I've moved on to a file based workflow, but when I was shooting DV, I would almost exclusively capture tape at a time for live events (needed fast turn around) and batch log for anything that wasn't a live event (wanted the organization).  I'd also typically still setup a batch log even for the full tape capture, just to maintain the DV backup of the video, even if it then required capturing the entire tape if I needed to recover the footage.