The pistons on this motor rise and fall together. That means both reach T.D.C. at the same time, but one cylinder will be on it's exhaust stroke and the other on it's compression stroke. You set the valves on the cylinder that is on it's compression stroke. To figure out which that is, watch the valves opening and closing as you turn the motor over by hand using a wrench on the alternator/rotor nut. I do the left cylinder first because it's easier to watch those valves as you're turning the engine over.
OK, start turning the motor by hand and watch for the left intake valve to open and close. Keep going and watch for the left exhaust valve to do the same. Now continue rotating until the left intake opens and closes again. Now start watching for the mark on the rotor to align with the T.D.C. mark on the stator. Also keep an eye on the exhaust valve. You want to align the marks before the exhaust valve begins to open again. That will put you at T.D.C. on the compression stroke for the left cylinder and it's valves can be set. If you miss getting the marks aligned and the exhaust valve begins to open again, you'll have to cycle it through it's opening and closing then continue on through the intake's opening and closing again. Then you can try to align the rotor mark again.
Once you get the left cylinder valves set, turn the motor through one full revolution and bring the rotor mark into alignment with the T.D.C. stator mark again. That will place the right cylinder at T.D.C. on it's compression stroke. Or you can go through what you just did, this time watching the right cylinder's valves opening and closing. But, you're on the left side of the bike while turning the motor over and that makes watching the right cylinder's valves difficult.
Once you get the valves set initially, you won't have to go through all this valve watching next time. Just set the motor on the T.D.C. mark and wiggle all 4 rockers to find the loose ones. Only the pair on one cylinder will have play, the other 2 will be tight. The loose pair indicate that cylinder is at T.D.C. on it's compression stroke and it's valves can be set.
