I have never seen a S2 switch ever go bad on a mep-004A. You can check it IAW, (in accordance with) the TM, but I don't think that's it.
The S9 switch, (Overspeed switch) is the beer can looking thing on the left side front door. You took a nice picture of it that I would have attached, if I was at home. It has a small button on the top to push in to reset the switch. Yes put the SP relay box back in. Does it look like anyone has fooled with the A4 card inside the control panel? Loose wires? Is the front or back side showing a burn mark? That's were K1 is and that has to work, for power to go to the places you don't have power. When you have the SP relay box back in and hooked up. Push in CB1, and put the S2 in the run position. Then see if the TT, (hour meter) runs. It should have a little arm that goes around and make ticking noises. You can also just use a multimeter and see if it has power.