Hi Dave We had a similar problem recently with a bike wearing a big straight through “silencer” that hunted / surged. Our guess was that a combination of an improved inlet gas flow had raised combustion pressures and was producing more energy. As original traditional ignition timing was 35 deg BTDC but with the 60 octane fuel of 1928 / 29, then the faster burning 97 octane fuel we have needs some retardation to say 31 BTDC, but if we combine this with an improved inlet flow, so that the cylinder is more completely filled, then the combustion is even faster so about 28Deg BTDC is a reasonable place to start. We do not alter ports but just concentrate on the inlet and transfer, but in the past, many folks raised the ports to improve power, but we think that this route gains power at the expense of the famous Scott torque. If the exhaust is noisy and it is possible that the ports have been lifted a bit, then the carb rejetting is a good start and if we are re jetting, we will always go a little bigger to be safe. You can always come down if it is a bit sooty. The most beneficial alteration we made was to fit a restrictor in the end of the exhaust pipe to give it a bit of back pressure. It cured the surging and made it more quiet. Do try the restrictor with an outlet hole of not more than one inch for a start and let us all know how you get on.
I know from experience with my racer that the exhaust has a very important effect on the performance of the engine and the different “Straight Through” modern pattern four stroke type silencers may just not be really correct for the Scott. For vintage era bikes, I would suggest contacting Ken Lack who is making a batch of Howerth silencers with fishtails. None of us are here forever and when Ken can no longer produce, there might be a few who regret not taking advantage while they could. Kind Regards