I sorta hoped there was some new wisdom out there on these carbs; most of my experience with them was pre-internet.
Okay, there's plenty of wisdom, you just have to accept it.
Start by making sure that you have the original tuning guide that Mikuni included with your carbs.
Then, recognize that your right wrist, as directed by your brain, is the most important thing, especially at small throttle openings and low revs. This is why God invented the CV carb, because most people send the wrong instructions to their right wrist. You can get away with this at 9,000 rpm; not so much at 900 rpm.
Then, remember I told you to clean the damn things and replace ALL of the rubber bits. Sometimes the path to success in not the shortest path chosen.
In the same vain, I'm hoping that you've verified that the float heights are correct and you measured them correctly.
Now, understand that you can't think of things in terms of engine rpm. That's CV carb thinking. You must think only of throttle position. When you say the mid-range is clean, thus the needle position must be correct, you are thinking like a CV carb tuner.
When tuning an RS carb, the first thing you do is disable the accelerator pump. There is a right way and a wrong way to do this. Do it the Mikuni way, as illustrated in your tuning instructions. Hopefully it hasn't been screwed with and is only starting to operate at 1/4 throttle. When you get done with the basic tuning, you'll want to start with the accelerator pump working in the range that Mikuni suggests. It's all laid out in the guide. For now, no pump for you
if I recall correctly, your needles have 5 clip positions. Put the clip in the middle position. I have no idea why it was raised one clip; put it back where it belongs.
Now, go ride the bike and don't use the throttle like you would a CV carb.
When you get back, dial the pilot screws back to the 1/4 turn-1/2 turn range and ride it again. If you have any access to a CO meter, use that (properly) to set your idle mixture.
You might also want to check for air leaks, everywhere between the cylinder head and carb throttle plates. If you have ANY
, fix those before going any further.
Make sure it's not so cold out that all of this is a waste of time at the moment.