It seems from reading your post that you have 3 questions.
1) It smokes a lot. So I guess you want to know what you can do about that.
Well I would initially suggest making sure your oil pump is set correctly (Assuming you are not on premix). Somehow I suspect that you have already done this, but it does no harm to double check I guess.
2) It runs rich at 1/4 throttle, so I guess you want to know what you can do about that.
Well,the air screw is set about right as per NSR-World guide,..here. And you have new slow jets, and I assume standard needles? So not too much seems to be wrong. Maybe,... maybe, if the oil pump is set way rich,... as it appears maybe the case??,.. then setting it correctly might fix your low throttle richness problem? That is a bit of a long shot, sorry.
3)Because you are setting the air screw with the airbox off, you seem to think that you may need to do something with the "pipe (plastic piece) that pushes into the bottom of the fuel tank". I'm sorry but I have never taken the tank off an MC21 so cannot help you here. But in the big scheme of things, I doubt that there is a HUGE difference at low throttle response with airbox on vs off. Please correct me if I am wrong,.. someone.
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[color=#808080][size=9]Yes,.. I too know how to waste Time and Money,...