I installed an MC2 on my S2R 1000. If you follow the instructions on the Web Site for 998 for the rpm connection (brown wire) it may save you debug time. You can follow the S4R instructions for the power connections and wheel sensor location. Using the yellow wire on the ignition box was not consistent.
My connections were the brown crank sense wire, negative wire directly to the negative post on battery, yellow wire on taillight assembly, and speed sense wire bracket on brake caliper bolt with the magnet on the rear sprocket.
I place the control unit under the left panel like in the S4R installation. It makes it possible to press the control buttons without removing the panel. This makes it easy to reset the rpm if ever needed and to put the unit into the learning mode.
Unit has been working great since the installation. I no longer look at the instrument panel when I ride. A majority of my riding is in the mountains with lots of elevation changes and turns. It is simple to look at cornering speeds for comparision.
I have not installed the radar connection yet as I need to get the power harness for my BEL unit.
Motion Research support will answer any questions you need if you have problems.
In case anybody does a search for this subject. For 2006 S2R - Yellow tail light wire to power, Black wire directly to negative battery terminal, and One of Three Thick Yellow wires to stator under seat to RPM wire. Hooked speed sensor to brake caliper with magnet to brake disc. Thanks for help.