All re-jetted 1100's I've been involved with had the DJ jet needles set at either the 4th or 5th position from the top...the majority at the 5th position. Test at 1/3 throttle position and get plug reads.
Drilling out the vacuum orifice to the diaphragm/piston chamber improves throttle response and is generally needed when re-jetting for your mods.
As for the stuck mixture screws, it sounds like removing them is going to cause further problems. If the o-rings inside were subject to carb cleaners, they are probably hardened/damaged and adjusting attempts may be useless. However, you can always try adjusting and see what happens.
The CV carb mixture screws should be adjusted using the highest rpm method, not by following a pre-supposed jet kit suggestion. If you're lucky, the adjustment range your semi-stuck screws are capable of may be enough to allow you to set them by the highest rpm method. With the larger 47.5 pilot jets recommended, you may find that somewhere around 1 1/2 turns out will work? Worth a try. If not, then you'll have to repair the screw adjustment problem to expect the pilot circuit to operate correctly.
Be sure the carbs are vacuum synched before getting plug/performance reads.
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