NC23 RRK vibration issues

[HondaCrank]

Hi everyone,
I have got an issue with a vibration. It did start with a knocking sound coming from the cylinders. I managed to solve that problem and then i took it out for a run and the vibration was signifcant. It comes through the handlebars, pegs and just the hole bike really. I know that it is not the tyres because before the issues they was fine and no knocking or vibration. Would a fuel/air mixture be a problem ? I only ask this because there is a different sort of noise coming from the air box. But if anyone has got a list of things that i could try and rule out that be of great help.
Also i have a speedometer issue. It reads slower than what i am doing. When i took the bike out for a run the other day i was doing around 60mph and the speedo was only reading 20mph. Any help with either of these issues that i have would be of great help.

[Wozza]

What have you done to it? What was the fix for the knocking sound?

[HondaCrank]

What have you done to it? What was the fix for the knocking sound?

I took the air box off and adjusted the choke. Then i checked the spark plugs, they were fine with the normal brownish colouring. Put it all back together and started the bike and no knocking noise. An hour later is when i took it for a run and i noticed the vibration. Oh and i forgot to mention that the knocking noise only started happening when the engine got warm