The ECU and wiring will most likely come with the engine. Only buy engine if you are getting the wiring and ecu with it. Otherwise dont buy. Since you will be putting it into the 2000 Civic, you might not need the wiring, but it depends which version of the engine you are buying and whether its ECU is obd2a or obd2b. The difference in both is that there are 4 slots on the ECU where wiring plugs are inserted. In obd2a, Slots 1, 2 & 3 (also referred to as A, B, & D) are used, whereas in obd2b, slots 1, 2 & 3 (A, B, & C) are used. So verify the ECU when buying the engine.
P2J-003/J11 are manual transmission ECUs, whereas most D15b engines that are available here will be CVT (automatic). So the ECU that will come with it will have code P2J-J61 (or J62).
I doubt if you will find engine with manual transmission and matching ECU.