"Since I've only done a few of my 17 tapes, I'm inclined to start over with batch capture instead of capture Now. "
why??
i prefer to capture all as quickly as i can, then log & sort it in FCP,
i also use media manager to break the long captures into smaller chumnks IF THE MATERIAL DICTATES.
yes, i re-name files as i go.
"On the other hand, some of the tapes have breaks in timecode"
not a big problem
but remember after a break to enter a new reel#
i also make simple notes on the tape case re the duration of each segment,
001 15mins
001a 30 mins
001b 10mins
this can help if you ever need to re-capture
a big question is if your program will require an on-line / off-line process.
if you capture as HDV, it's likely you will not, and you will be cutting with what you send to the "on-line"
so as to avoid having to re-capture due to some drive failure, always have backups.
nick