I'm not sure if it'll help in your situation, but you can put site-specific replaces under the site section.
Code:
[www.fanfiction.net]
add_to_replace_metadata:
# Characters
characters=>^Garrus V\.=>Garrus Vakarian
characters=>Tali'Zorah=>Tali'Zorah nar Rayya
characters=>^Martin S\.=>Martin Septim
## ffnet's Mass Effect section screwed up when trying to merge the two Shepards. May need occasional storyUrl override.
characters=>^J. Garson$=>Female Shepard
characters=>^Shepard$=>Male Shepard
My thinking is that this would allow you to split apart the regexes to two simpler (and hopefully less breakable) ones.
Addendeum: One neat thing is that while you can only have one conditional, the siteUrl section itself kind of counts as a free
&&publisher==FanFiction.net conditional.