Hi again, hope you are all keeping well.  Thanks again to everyone who helped point me in the right direction on the ignition side of things.
Now that seems to be resolved I am looking into whether my RT2 might have a common problem in the gearbox.

Riding hard up through the box once we get to 3rd the experience is as if it is stuttering - a noticeable drive/no drive kind of thing. 
The revs dont skyrocket as if in neutral. 

The gearbox was rebuilt a couple of years ago with new dogs etc

Could this be down to adjustment on the selector? Or is it sounding more severe?

Ideas please - many thanks

My first thought on this issue is always the cam stopper (see items 19-22 on the attached).

Is everything in place and is the spring "springy"?

The bolt is situated on the underside of the engine, is often mistaken for the drain bolt and therefore the parts fall out and get chucked away with the old oil! 

yamaha-rt2-1972-usa-shifter-a_bigyau1202b-2_5ac6.gif (1099×1500) (cmsnl.com)

Good idea, I will check this. 
I know that the screw is in place underneath 

Only one answer in my book, knowing how we used to destroy third gear motocrossing & that's dogs on both mating gears are rounded off & ramping out & has blued & bent the selector. Or if you're very very lucky the sprocket nut is undone so the shaft has moved over but that's not likely or sprocket would fall off. Sorry about that chief. & hope i'm wrong. Could increase spring pressure on the plunger although i'm not recommending it as will only increasing damage already done in my opinion, as will still be trying hard to jump over doggies & bend the selector even more so.

The gears affected are 20 going into 21 despite what they might be called in the parts list. Plus the associated selector of course. & something i forgot but can easily find a selector drum to demo, the high point of third becomes chipped & dented so reduces engagement. If this is overlooked on rebuilding its all downhill from there. But if its undamaged then--bonus. 
www.partzilla.com/catalog/yamaha/motorcy...972/rt2/transmission

Yes, there was a Yamaha service bulletin on this I think...

It was something like you put ink on the high spots of the shift drum and roll it on a piece of paper. It will give you a "print out" of the guide grooves.

Then you do the same with a brand new drum and compare the two prints.

...maybe I'm thinking of something else the bulletin was for other than wear... but they did have you compare ink prints.

But as RT325 said drum and fork can be overlooked and the damage to gears can happen again sooner than it should.

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A completely different thought about your problem, but might be worth checking your countershaft sprocket, to make sure it isn't completely worn out. Carry on chasing tranny issues if it isn't that.

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Good point EN...  At one of the Hungry Valley events a few years ago we worked on Husky Dave's bike for hours trying to figure out what the heck was going on.  He was having trouble on the steeper hills with bike jerking and no power and was making a strange sound.  We never did figure it out that day.

When he got home he pulled the side cover and found the teeth on the countershaft sprocket had worn down to nubs.  Chain was slipping on sprocket.

"When he got home he pulled the side cover and found the teeth on the countershaft sprocket had worn down to nubs.  Chain was slipping on sprocket."

Trying to load pics & wouldn't & now lost what i wrote damn it. Try later.
Ok, tried a different way fingers crossed.Trying to load pics & wouldn't & now lost what i wrote damn it. Try later.
Ok, tried a different way fingers crossed.