I've got an S&S Super E myself so I might be able to help a little.

Let me think about this a little while.

But while I'm thinking, let me ask you about the condition of the carb. Have you pulled it, disassembled it and rebuilt it?

If so, have you checked the throttle body at the orifice where the mixture screw penetrates?

Some gorillas crank down on that idle mixture screw when they are closing it, and they crack the throttle body (ask me how I know) and when that happens, the carb is almost impossible to get right. So check that out.

Also, in my '93, I had excessive carbon build up inside the intake ports which kept the bike from ever running properly. Carbon build up on the intake ports and backside of the intake valves will cause a false lean condition when the bike is cold, and then a false rich. The carbon absorbs a lot of the fuel while the engine is cold and the bike runs lean, so people adjust the carb thinking their lean. When the carbon has absorbed all the fuel it can hold, it causes a rich condition by releasing vapor that's not needed. It really forks up any attempt at proper tuning.

If I were in your shoes (and I have been), I'd pull the carb, rebuild it (kits are $40 or so depending on how far you need to go) and check the intake ports for excessive carbon build up. I'd then get some new intake gaskets, remount the carb carefully and proceed with the tuning process.

If you need a new throttle body, you may just want to buy another carb. Throttle bodies are about $300.

My throttle body was cracked and I lucked out finding a new-condition one on E-bay for $80.