I don't think its a fair assessment to compare your ability to control the chlorine with the out of control pH vs in control, so let's deal with the current conditions. The Intellichlor operates in 6-7 LED increments, so you're not able to fine tune the output of the system unless you're running the salt system through an in-house electronic control system (like the intellitouch).
1) Are you controlling the Intellichlor through an Intellitouch?
2) How many hours per day is your pump running?
3) You mentioned that your colorQ test was different from the store test results on the pH. How much different was it?
4) Staining - What color are the stains? and do you have a heater?
5) Have you added any algaecides, clarifiers, metal removers?