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Yamaha sr-125 low rev problem - is it fuel or electrical?

My Sr-125 starts misfiring at low revs so I'm unable to cruise - the bike needs to be constantly 'pulling', which isn't good for petrol consumption or the engine. Sometimes the misfiring can get so bad, the engine cuts out. It never restarts straight away but its able to after it's been left a minute. This made me think it was an engine flooding problem but there's no visible overflow or smell. I took it to the garage and they cleaned the carb, put in new ignition coil (in case it was electrical) but still the problem persists.

However, yesterday I put in premium grade fuel (by accident) and the bike runs 90% better. It still misfired a couple of times at low revs but no where near as bad.

It's only a 1999 SR-125 so doesn't require premium grade so what possible problems could it be?
The problem is longstanding for months now so water in the tank isn't the problem.

The bike has had new spark plugs, ignition coil, carburettor cleaned and a standard service recently.