The low speed fuel screws are adjustable for a reason. So you can get the best running. Seems pretty obvious to me that you should try and adjust them to help with your rich mixture at low end. After all the screws affect low speed running mostly. To set them to a standard position means that you are hoping for the best but not actually tuning the mixture for best or most efficient running. I wouldn't worry about having marginal cooling if your gauge is reading normal. After-all you are only needing 50% of your normal amount of power.
I have adjusted single groove needles on many bikes. Some of them have the needle mounted in a clip that you can reverse or remove. If you want to lower a needle that sits in the slide without obvious means of adjustment try cutting the top of the hole of the slide letting the needle sit deeper in the piston. Many times a mm of adjustment is plenty. You just have to reverse engineer. Sudco may well sell alternative needles. You may have to measure the diameters every 10 mm and compare them to the charts on their web page.
Your bike probably won't be near stock as you are trying to do different things than it was designed for.
As for spark timing some advance from stock is a pretty standard way of improving response and economy. It can lead to trouble with high temps if you run it hard I doubt if you are. It moves the pressure peak up a bit.
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