I did the same thing removing the 2nd O2 sensor, EGR, charcoal canister, etc.. The factory ECU will run fine. Obviously with the check engine light on. I did go with the MS3 right away once I confirmed engine and electrical system worked fine with factory ecu. Don't throw away those extra wires and connectors. I know I used them later in the build. For example, I used a connector for all the wiring going to the rear of the car.
Wiring looks great. Build gets a little more fun again (you see more progress) once you get passed that hurdle. :-)