The MPS unit is very user friendly. So Lets try some troubleshooting. Get out the old voltmeter and check to make sure your switched hot is hot while the bike is running and not just hot at start up. Then insure that the box's ground is going to a good engine ground. I tried a frame ground on a Busa once and was not getting a consisstant (spelling?) ground and the shifter would work sometimes but not all the time. So I used an engine bolt for the ground and it worked great. There are 4 brown wires, but since we are runnings twins you only need two, but if you do not get enough delay you may need to take the other two wires and connect them to each of the ones connected to your coils. I did not need this on my 996 so you should be good. You said you tested your switch and it is good so now check to insure you have continuity to ground when the switch is activated. Take the ohm meter and set it to continuity and then take one lead and connect it to an engine bolt and take the other lead and connect it to the ungrounded switch wire. When you pull on the switch you should get a beep from your meter showing continuity. If all this looks good it may just be the coil connections the unit works by grounding the posative signal sent to the coils. My 1098 is a the stealer for a warrenty recall, otherwise I could check my coil leads (they are the same as the 999/749) but you may need to recheck that connection. This is best checked with an analog volt meter, connect the black lead to ground and use the red lead to check each wire/terminal on the coil connector, when you have the correct lead the needle will jump on the meter. it will not stay hot, is so you are on the wrong wire. It will only go hot when the computer fires the coil.
Try these things and if you still have trouble pm. me and I will pm back my number and we can go over everything. I have my old 996 that I sold a friend in my shop so I can look at how I have things connected and check voltages on it for you if you need it. Don't get discouraged the MPS unit is a good very durable unit. We will get it figured out.
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