My 71’ RT1B now kicks back when I try to start it.
I took the head off mounted a Dial indicator , Wedged the Centrifugal  advance open  ,  the point gap is .014 thousands And the points open at 5.8 mm BTDC Instead of the 2.9 mm that it should be at. The flywheel key is intact and is not damaged or loose, The advanced mechanism moves freely and is not worn or
Is it possible to crankshaft stub has spun in the crankshaft half? , Thanks, 

No chance of anything spinning as crank half is one piece of steel.

Timing is set by adjusting point gap.  You never set points to a spec like 0.014" if you want the timing correct.  

How are you determining exactly when the points open?  Critical to make sure you have an accurate method of determining point opening.  Magneto buzz box (about $80) is great.  Or an analog ohmmeter with an Rx1 scale (can be found for less than $20) work well.  Eyeballing does not work.  

After timing is set to spec, then you can check the maximum point gap which should fall in the spec range of 0.012" to 0.016".  If it doesn't, something is wrong, do not adjust the gap to a spec or you will screw up the timing!  I generally set the 360 slightly retarded at 2.5 mm BTDC or 0.100".

If gap not in spec and you've double checked everything, then the next step is to replace points with OEM quality parts.  Yamaha factory points or Daiichi aftermarket are the only ones I'll use.  

I'll read later on my desktop but my guess is crank key ie flywheel key is damaged or broken & flywheel has moved. Points gap will still remain same but piston is in the wrong btdc. Use the proper puller 27x1 left hand & tighten flywheel TIGHT or tighter than that even or they let go & destroy the key.

Thanks for the reply and the advice, I used an ohm meter
to find when the points opened. Flywheel key was undamaged and intact, the flywheel slides on tight and
my points are almost new. I tried adjusting the point gap and it didn’t get it anywhere close, any way I resolved the issue by taking the stater plate off, drilling holes on the drill press to make it slotted. I then put it back together, and I had to move it a half of an inch to get it correctly timed and now it runs perfect! 

 

Thanks for the tip On tightening the flywheel nut And keeping it tight

Well that's good news an very interesting as in theory it doesn't add up as to why all that was needed. In my mind I can imagine the crank bent or out of true big time so its revolving in a big arc & arriving sooner than planned at the points. I dream a lot lol. Arm on the sdvancer not broken in respect of how it's limited on full advance?. 

photos.app.goo.gl/34UXYPM5APVbhvSb7

The flywheel advance mechanism was fine. Nothing bent. I actually had another flywheel to compare it to in both were the same. I kept thinking that somehow the clocking was different on my flywheel in relation to the location of the key slot so.
I have worked on vintage motorcycles for decade, but not many of these Yamaha enduros. This was the most bizarre timing issue I ever came across, I can’t figure it out either, but I did know how to fix it. . there was more than once where I thought the Kickstarter had broken my foot!!
 

If you have a '71RT1B (black with red pin stripes) with a decompression valve on the front of the cylinder then it is possible it came without the mechanical advance/retard flywheel. The '70 RT1 (black with yellow pin stripes) did not have the decomp valve but did have the mechanical advance/retard flywheel. The stator plate is different between them and must match. If you have the wrong stator plate that might be the reason you got it fixed by drilling it.

Timing is set by point opening, not point gap.

Point cam may be worn being 50 years old.
Point set lever ratio may not be to spec.
Both of these things affect point gap.

Buzz box or meter(slowly) should show opening point.