I'm posting this on behalf of a good friend in Australia, hoping the collective knowledge can offer a solution; here it is in his own words. He has posted a video on You-tube describing the issue so feel free to comment on there if you wish, otherwise I'll give him the link to here.
"My S&S Super E carb has performed flawlessly for several years, kickstart only, with one issue. I replaced the throttle shaft and plate about 5yrs ago as part of a general overhaul of a tired carb, and ever since I CANNOT get the throttle plate to to return to its fully closed position *IF* the accelerator pump screw is even slightly ''on''.
So I have had the accelerator pump switched OFF. No squirt of fuel when I twist the throttle ... But the alternative is a high and erratic idle because the accelerator pump is ON thus the throttle plate does not shut.
I have lived with it, but now it bugs me and I want to sort it so I do have a working accelerator pump at the same time as a perfectly closing throttle butterfly.
I have cleaned the carb thoroughly (you can see how gunky it has become in 5yrs by looking at the throttle shaft along the plate, I will get a cotton bud into there to finish the job)..... checked the little balls and spring in the accelerator pump housing, the shaft and rubber boot are clean......what gives?
Any solutions welcomed. At this stage I feel like I will buy and install an accel pump rebuild kit, at least....
There is no issue with throttle cable adjustment, trust me. I have adjusted it 56 ways through Sunday....."
Thanks in anticipation for your help
2005 XL1200R.... well ya gotta have a rat-bike!