Thought I might just chime in cause there's a bit of stuff in this thread that kind of contradicts my understanding of two stroke tuning and I'd like to clarify a few things/contribute to the knowledge base (and I may very well be wrong... but this is what I learnt from tuning my RD). Jetting a smoker doesn't start at the main jet - the main jet is only ever really effective from 3/4 to full throttle (it does start to come into play at 1/4 but its effect is gradual). Before this, it's your needle jet/needle and pilot that do all the work. Jetting a two stroke should really start at the *pilot* jet (assuming your needle jet/needle is set up right - this is another matter). To do so, you warm the bike up to operating temp, then at idle you turn the air screw until you find the point of highest idle.
The air screw should be no more than 2 turns out and no less than 1. It varies a bit from bike to bike, but my RD, for example, should be set at 1 1/4 turns out according to the factory spec. You might find that with today's fuel and changes in altitude you might need to go up on the pilot jet a couple of sizes (I did). The point of this is to obtain the correct air/fuel mixture at idle, which will effect the running characteristic right across the throttle range. You can further tweak the air screw to get the perfect response when you crack open the throttle, too, just by riding and turning it an 1/8 of a turn.
Issues with low end running can usually be attributed to the pilot circuit and needle clip position... The main jet size should be determined *last* and the easiest way to do so is via the plug chop method, which should only ever be done with brand new plugs or you'll get an incorrect reading. If you change the main jet before you correctly tune the pilot/air/needle position, your main jet will be off... but, most importantly, before you do anything to the carbs, clean them *thoroughly* (and I mean thoroughly), or all your efforts will be in vain.
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