I've started taking practice tests (thank you, jlpt.info) for 2kyuu, and getting each section to add up to 100 points seems a little opaque. For instance, the 1991 test has:

-Bunji/Goi: 65 questions, 100 points
-Choukai: 24 questions, 100 points
-Dokkai/Bunpou: 50 questions, 200 points

Any clues as to weighting some sections more than others, or is it just the percentage converted to points?

(Either way, I've got work to do. Those fill-in-the-blank bunpou questions took me down.)

Each vocabulary question is worth twice as much as one kanji question.
Each reading question is worth 5/2 as much as one grammar question.
Listening questions are weighted equally.

Thanks, Jimmyseal-- by this equation, I passed by 8 points! Still, work to do.

here's the official scoring formula from the 2006 2級:

文字(pronounced moji, btw)/語彙
problems 1-40: 1 point each
problems 41-65: 2 points each
divide correct points by 90 and mult. by 100

聴解
problems 1-27: 1 point each
divide correct points by 27 and mult. by 100

読解・文法
problems 1-21: 5 points each
problems 22-56: 2 points each
divide correct points by 175 and mult. by 200

if your point total is 240 or more you pass!