#1, the 9000 valve... are you sure it is not a 9100? The 9000 is not my favorite valve. The brass body is not as durable as the 9100's plastic valve body in certain water conditions.
#2, the valve should not have any safety factor, set it to 0. The system is a twin alternating design and should use close to 100% of it capacity assuming you have it set to regenerate immediately, not on a delay. A delay would not make any sense for a twin alternating system in the vast majority of applications.
#3, Do not use the manual to determine the salt fill rate. Fleck makes available refill rates of .125, .25, .5, and 1.0 GPM for that valve. On the valve where the brine line attaches to the injector/drain assembly, you will see a sticker on the valve. It is typically red, blue, or black. Read it, it will tell you the refill rate. Assuming your system is set to 6 pounds of salt per cu. ft, your system capacity should be set to 20K per cu. ft, or 50K. 6 pounds per cu. ft. would require 15 pounds of salt, or 5 gallons of water.
Hope this helps.