Hmm.. I have the same problem as narahttbbs, in that the only fanfic I tend to read ever is XF-based.

It's not fanfic, but have you ever read Greg Egan's Oceanic (http://gregegan.customer.netspace.net.au/OCEANIC/Complete/Oceanic.html)?
It's biochem-ish SF with religion.. I've no idea if it would be your thing really, but I think it's fantastic :-)