I'd like to offer a machinist's view on the actual purpose of aligning the pressure plate with the clutch boss, and why there is only one way (unless, by chance, you get very lucky) that the two can be assembled in order for the clutch assembly to operate properly. It's strictly a matter of the manufacturing processes involved in mass production.
If you look at the backside of the pressure plate it's obvious the six as-cast cups that hold the clutch springs, fit into the six as-cast pockets of the clutch boss. The drilled thru-holes in each of the pressure plate spring cups also has to fit (without interference) over each of the as-cast clutch spring screw bosses.
What's not obvious, when correctly assembled, is that there's only a very tiny amount of clearance between the six as-cast pressure plate spring cups, and the six as-cast pockets and screw bosses of the clutch boss itself. But it's enough.
The clutch boss and pressure plate are castings which can vary in dimension from one batch to the next. To maximize profit, production machining fixtures are designed to not only accommodate this casting batch size variation, but also enable as many machining operations as possible without having to remove the part from the machining fixture.
If every surface of the clutch boss and pressure plate were machined, then having to align them wouldn't even be necessary. But production = profit, so only those surfaces absolutely required for a part to fit and function get machined. It's the unmachined, as-cast, surfaces that make it necessary to properly align these two parts.
In the case of "mating" parts like the clutch boss and pressure plate, machining fixtures also have to provide a means of accurately "indexing" two different cast parts, machined on two different fixtures, in such a way that there's no interference when the individually machined parts are assembled as a unit.
From the beginning design stages of the clutch assembly, right into production, obtaining clearance between as-cast surfaces is accomplished by each individual part of the assembly, and every machining fixture, being referenced from the exact same "zero" reference point on the master assembly blueprint.
The "zero" reference point for the clutch boss is shown in the first photo seen below. It's not voodoo, it's simply the reference point that all production casting and machining operations, to both the clutch boss and pressure plate, were indexed from. This also ensured that there was adequate clearance between all as-cast surfaces of the clutch boss and pressure plate when assembled.
I think some of the confusion revolves around the fact that the clutch boss has 29 teeth and 6 spring screw bosses. Since 360° is not equally divisible by 29, and 360°/6 = 60° is an equal spacing, it's standard design practice that the center-line of one equally spaced (60°) spring screw boss should be aligned to the center-line of one unequally spaced (12° 24' 49.66") tooth.
If your clutch boss doesn't have a marked tooth; use a 6" steel rule to help you sight a line from the center-line of the splined shaft through the center-line of a screw boss, that hits dead center on a tooth.
The center-line of only one tooth and screw boss will line up exactly with the center of the splined shaft. Mark that one tooth with a light center punch for later reference.
The center punched tooth is the "zero" reference point that the earlier style stamped "OK" mark or the later style drilled hole, found on the face of the pressure plate, must align with.
Clutch Boss "zero" reference point:
Earlier style "OK" stamp mark aligns with Clutch Boss "zero" reference point:
Later style drilled hole aligns with Clutch Boss "zero" reference point:
You might ask; Why didn't Yamaha just include a cast alignment arrow on the face of the early pressure plates? As a machinist I'd say it probably had to do with the size variation in castings, which determined how the rough pressure plate casting was oriented in the machining fixtures. If it didn't fit right you pulled it out, rotated it 60°, and tried it again until it did. This early casting, and machining setup would pretty much negate having a cast marker.
When the machining operations for producing the clutch spring seats and thru-holes was completed, the machinist took his hand stamp, lined it up with the "zero" reference point on the machining fixture, and stamped his "OK" symbol on the outer face of the pressure plate as an alignment indicator. In later production a much improved casting, and machining setup did incorporate a cast arrow mark that the alignment hole is actually drilled through the middle of. These engines were built well before CAD/CAM and robots.
About the "OK" alignment symbol on earlier pressure plates: In my career I've met machinists from many countries and we all love putting "our" mark on a finished workpiece, even if it's just stamping factory serial numbers and alignment marks. I've looked at several of those little symbols under magnification and I'd swear it represents a left hand that shows thumb, index and middle fingers forming a circle around a center mark, with the ring finger and pinky raised.
