You have to remember that you set the floats with the carbs upside down, so setting the floats "lower" (to a lower number) is actually setting them HIGHER when you turn the carbs over.
Yes, the level of the fuel does affect whether the mixture is rich or lean. If the level is higher (lower number when you made the adjustment), it is easier for the air passing over the jets to suck up some fuel, making it a richer mixture. On the other hand, if the level is lower (higher number when you made the adjustment), it is harder for the air passing over the jets to suck up some fuel, making it a leaner mixture.
Since you verified the level with the clear tube, it should be fine, assuming it was at the proper level.
Do you have the stock airbox and stock exhaust, or has either one of them been changed? If they are both stock, stock jetting should work just fine. With today's ethanol-laced gasoline, one size up on the mains, shimming the needle (by removing the plastic spacer and replacing it with a shorter stack of washers, as outlined above) and another 1/8 turn out on the pilot screw should have the carburation set just about perfectly.
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