I just completed this entire procedure: Canisterectomy, SAS removal w/ block-off plates, resistors to fool the ECU, da woiks. I connected the intakes, using the original fittings and a short length of discarded hose . . . never even tried it with the intake holes blocked with bolts.
Yes, the front cylinder's block-off plate is a PITA to install. I removed all the bolts that hold both the oil tank and the radiator, so I could moved them out of the way (just enough) to reach both block-off-plates bolts using a u-joint w/socket.
Also just replaced chain and sprockets, went to a 16T up front.
The bike is transformed: Better throttle response, yet better control at low speeds, runs smoother. It's a happy bike.
Thanks for such a great post.