Get one of the recommended test kits, with the salt addition. Readings on the generator itself can be pretty far off. Best to use a standardized, repeatable, test before making adjustments. Believe the test kit far more than the reading on the generator.
As noted, the salt never goes away. It may increase slowly IF you have to augment with liquid or other forms of chlorine beyond what the generator makes. The only way to lower is to partially drain and replace with fresh. Check your manual for the range of salt needed for your generator - while 3900 may be highish, if it is in the range the manufacturer calls for, you are fine. Higher or lower (if in range) doesn't effect the overall output of the cell.
The generator will make a maximum amount of Cl if run at 100% in 24 hrs. The max is variable depending on the make/model of your generator.
If you set it to, say 50%, it will turn on and off by itself, to reduce its 24 hr maximum by 50%.
Turning off your pump will shut off the SWCG. So running the SWCG at 100%, but only running the pump for 12 hrs, gives you the same 50% reduction in Cl - since the pump was off for 50% of the time. Pump speed doesn't matter, only whether water is flowing or not.
You can therefore balance the amount of Cl made by either method - cell % or pump run time. Or by doing both.
Many of us, if the pump has variable speeds, will run the pump 24/7 at a very low setting to save huge amounts of energy. And then just adjust the SWCG setting to give the amount of Cl level we want. While the speed doesn't matter for the generator, you may have to (or want to) have the pump a little above the lowest speed if you have items that won't function on the slowest (heaters, water features, skimming of surface debris is poor, etc.)
Finally - the setting you find for your SWCG will vary during the year, proportional to the amount of daylight. So going into winter, you may need to dial it way down, but in summer it may need to be dialed much, much higher. For mine, during summer I find 60-70% is perfect. This time of year, 20% was almost too much. Your numbers will be very different from mine, though.