Update - cleaned the carbs again and swapped all jets. Found a small tear in the air solenoid tube. Started her up and still the same - she struggles returning to idle. I then checked the exhausts and the bottom cylinder was hand warm whereas the top was too hot to touch. I checked the spark and she has a good spark but still misfires on the bottom cylinder. Also noticed petrol and oil being thrown out of the exhaust of the bottom cylinder.

Next step is swapping the coils (albeit both are new and had used them in the bike before the rebuild). If that is not changing anything then I will swap the PGM CDI.

Any other suggestions?