I'm using the 50 pilot jet and it seems to be the right size.
Here is the new plug after 5 minutes riding with some WOT pulls up to 4th gear.

Pilot screw set on warm engine, best idle at 1.75 turns.

Here is an image of a new plug yesterday, after an hour of riding through the hills.

Mystery rich condition update.

80kms today of pretty varied riding from slow and easy the hectic revs throughout the hills.

I raised the needle with 4 washers, no spacer.
This picture is the plug after the ride.

I am still struggling with the flat spot/sputter at 1 to 3 percent throttle. Changes to the needle height have had zero impact on this. And it is now the only problem with how this bike runs.
But some more detail on this was discovered.
It is most prevalent when coasting down a hill in a lower gear/ at higher coasting revs. When I touch the throttle during this time, there is a stutter.
However if I go up a gear and lower the coasting revs, the issue is less apparent at that 2 percent throttle. Go up to 4th and it's gone entirely.

So it appears it's really only an issue at those higher revs.

Hi Mike.

The TEV and diaphragm are clean with no holes. . I've been zip tieing the plunger in place when I ride. Just cut the tie for the photo. But I'm still looking for another.
The bike is riding really well. There is just this last issue I'm chasing now. Hopefully I can find another plunger assembly but I don't think that will fix it unfortunately. It feels like the slide is just hesitant at the start.

Update.

With the new plunger Installed the issue has unfortunately shown zero change as I thought it may. My pilot air jet fits a 0.6mm drill bit however, even tho these are numbered, they are cheap bits from Amazon and I'm not sure I trust them to be super accurate. I have 3 of each size and they all felt different with the shaft end in the main air bleed.

As it feels like the stutter is where the carb goes from pilot to slide, I tried raising and lowering the needle. While this changed how the bike ran , lean or rich at that throttle range, it did not alter the 1% throttle stutter. So maybe the issue the pilot circuit somewhere.

I can idle along very slowly without any problems. And the bike is certainly rideable and rides very well.

This is just the final little issue I am facing and is mainly an issue when down shifting and coasting where I first apply throttle.  
While adjusting the needle I noticed a small resistance or bump when raising the carb slide by hand. Doesn't feel 100 percent consistently smooth at the start.

Hi Paul. Yes I replaced it. I mentioned it in the last post. I called it a plunger assembly as that's what it's called in the parts diagram.

It idles great now. It's just the stutter when coasting with the revs up and just barely touching the throttle that's the issue now.

That "small resistance or bump" you feel when you raise the slide by hand may also be a problem.  That could be hard to rectify.  Your carb is really old and the photos show it is in very poor condition.  If the slide and carb body are severely worn it might not be salvageable.

Also, there are two air bleeds in the top of the carb.  These air bleeds are for the idle circuit and the transient enrichment circuit.  On your older carburetor, one of those airbleeds is just a fixed hole, the other has a removeable jet.  

On your carb, the fixed hole (circled in green) should be 2mm, and the jet (circled in yellow) should be a #70 (about .028").  You may be able to improve the condition by playing with the pilot air bleed jet (the one circled in yellow).  A smaller jet will make the mixture richer, and a larger jet will make the mixture leaner.

These are the pilot air bleeds in question.