Scosche has quite a few wiring harnesses to help bypass the crap in a civic. Go here to see if they have anything that might be helpful. I bought a harness from this company when I owned a '97 Civic.

http://www.scosche.com/applications.aspx

I just bought an OEM keyless entry/alarm system for my '99 Integra... it took quite a few hours to install... like 6-8 hours. It required me to remove the nose of my car to mount the siren in an place that no one could get to it. I also had to mount a switch in the hood. It was a bear to install, the area under the dash is tough to work in, but the thing turned out perfect. I am quite pleased with my purchase/install.