Your transmission will bolt to any other D series engine. That would be all Civic engines except the Civic SI.
Yes, there is a standard wiring harness. It connects to the rest of the vehicle at the firewall near the battery and near the brake booster on the drivers side. However, your harness is slightly non-standard (only due to the O2 sensor). You can modify it and make it work, or you could use the wiring harness that matches the motor you are installing.