Whew! Okay, I found a solution for what I can do!
The trick is to convert from PDF to CBZ first! Once it's in cbz format, then calibre can convert it! I end up with a watermark, but I don't mind that. There is a comic converter for that here:
http://www.jontylovell.net
It isn't a perfect solution, the converter produces a 100MB CBZ from a 10MB PDF, so it's slow and takes a lot of room. But the resulting EPUBs for my nook in the end are only 3MB. Even better, these programs both handle batch operations, so I can throw a hundred in at a time and let it run overnight.
So anyway, I know this has nothing to do with Briss, but I figured someone else might have the same issue later and would want to know a solution.