There is a short guide for the conversion in a civic out there...I saw it and skimmed through it a while back, but I didn't save it or bookmark it, sorry.

Really though, selling your car and buying a manual is probably cheaper and less of a hassle. That said, I have performed a similar swap in an older BMW...
http://www.e30sport.net/viewtopic.php?t=10427
http://www.e30sport.net/viewtopic.php?t=10590

I imagine it could be both more complicated and less complicated in a civic.