You have to use your Civic wiring harness on the LS motor, the LS is a 2 piece harness and the civic have a 1 piece harness. I did this swap on my 98 civic. You aslo need a b16 rear mount, and a b16 front uppper mount.
B series axles, and a B series shiftlinkage is needed too. And you would also need an OBD2 LS motor to go into your OBD2 civic, Unless you get a conversion harness and convert to OBD1. You would also need to do some wiring modifications.