Guesses and no more.
Spitting back from the high compression cylinder, also seems to be running rich on the same cylinder.
This is the cylinder with the mis-fire. Its unable to burn the fuel from two cycles and chucks some down the exhaust and turns the rest into carbon.
That is why it has the highest compression ratio.
It is also like to be the one with the cleanest looking bore from fuel washing.
Very likely that this cylinder has no valve clearance on the inlet.
If this cylinder shares a coil with the other cylinder which appear rich then it is coil or dyna components. If it is a different pairing it is plug or lead.
Also getting backfires from the exhaust, bit harder to tell which cylinder.
Its the one above which appears to be running rich!
Have been thinking a bit more about this, its possible there is a electrical problem (feed to coils), but from what I remember there both share the same possitive feed.
Dont know dont do electrics specially not with a crystal ball.
Its done quite a few thousand miles since it came back from Spain, including a one day quick ride to Sweden (almost 1000miles) where it went with no problems.
Tempted to say that this is different fuel but really dont know why.
The exhaust ports colour two black one fairly good and one brunt white.
Two black on the same coil??? If so timing out or feed to coil intermittent.
What does 'one fairly good' consist of? If you mean dark~ OK
'One burnt white'. Low fuel level, incorrect valve clearances, leak at inlet manifold, leak at exhaust manifold fuel bypass screw to far closed or blocked.
Assuming that the 'one fairly good and the one burnt white, are the same coil i would suggest that the timing overall, or for that pair only, is / are retarded.
Cams none standard but could not say what they are
If you dont know i sure as shit dont
I hope this helps. If this ever goes to court i will naturally deny that i said any of this.
Let us know how you get on or if any of this makes any sense for your situation.
What were the valve clearances when you took it down? What motor is this by the way and which cylinders and pairs of cylinders are you referring to? It would have been much more help to others looking to help if you posted details and / or pictures of the situation but its not too late.
AL