more Q's

i'm trying to get this bike to start without even a putter. i have spark and supposedly the timing was never altered from when it was last run in 82. so i get the RH cylinder to compression using the thumb pressure method, bump the wheel to 28 degrees under the inspection cover. Now points are new to me, and i have been reading everything i can, but according to the shop manual there's a scribe on the rotor. i see a definite notch, then the scribe like 1/8" by it. line that scribe up with the tip of the nylon points guide and that side should be open at max, then spark occurs. From what i see, that scribe in the rotor is almost 180 off from where it should be. no amount to retarding or advancing the plate will even get me close.

LH coil is yellow/black RH coil is white/black, the yellow/black wire should be at the point farthest to the rear under the timing cover. I know i have what wire goes to each cylinder right.

So what am i missing here?

First, set the points gap on each set of points to 15 thou by lining up the heel of each points set with the scribed line on the auto advance unit cam (not rotor).

The scribe line then has no further use for ignition timing setup.
The ignition spark occurs when the points just begin to open, so it is this opening point that is set to 28 degrees with the AA unit locked fully advanced. You will need to use a bulb or meter to accurately set this statically. And strobing is a better way to do it.

Are you locking the auto advance unit at the fully advanced position (bob-weights out)? As you need to do this first, otherwise you cannot statically set the timing at the fully advanced position?

If the setting seems to be 180 degrees out then you may be setting the points for the wrong cylinder although your description of the points wiring seems to be correct? Possibly the auto advance unit has been installed 180 degrees out and needs to be moved?
The engine would still have run with the AA unit in this position if the points wires had been swapped over in the past?

You may be aware that there is a 3/4" hex timing plug in the crankcase below the timing cover on the Mk III which can be removed to more accurately check the 28 degree BTDC position (look for a slot as you turn the crank) as the timing scale in the primary case that is generally used for the ignition timing may not be totally accurate.