Fish is correct. A JDM engine is RHD so the battery/fuse box and ECU's are on the opposite side of the car so the stock JDM wiring harness on the motor is useless except to salvage plugs and wires. You can remove your old D-series harness and modify it to work (how depends on what model Civic you have).

You will also need the items you listed, B-series axles (there are 3 pieces), B-series shift linkage (D-series will not work) and there are several mounts you will need. You need the big silver mount top engine mount (coming out of the timing cover). You will also need the lower engine and tranny brackets. You can re-use the Civic rubber mounts on the bottom of the frame rails. You can re-use your Civic mount on top of the tranny. For the rear, you need the B-series T bracket and re-use the Civic rubber mount on top of the rear subframe. You'll also need a GS-R throttle cable and make sure you also replace all the belts and radiator hoses (cheap insurance). Good luck with your swap. Seeya.