Three factors are involved with answering this question. The first is how low or how high is your watt setting the higher the watt setting the longer auto-tuning takes. The second factor is ambient temperature. I have found that if the ambient temperature is cool and controlled the process is much quicker than if the mining environment is a hot garage with little ventilation, for example. The third factor in "how long" is the condition of your individual chips. Since auto-tuning tests and sets levels for each chip, if you have a well used S9 which maybe has lots of debris in the heat sinks, thus damaging some of your chips prematurely,  or if you have overclocked your S9 beyond factory specs, it is possible you could have weak or damaged chips which will take longer to tune because they intermittently fail thus causing the auto-tuning to change it's values.

What models and how old are the S9s you are tuning? What is the watt value you are putting on the configuration page? "Horrible hashrates": When the tuning process is on it's last steps it begins "tuning individual chips". The hashrate gets significantly lower when this process begins. I have had rigs take 5 hours to auto-tune at 1200W and 2 hours at 900W. If you are overclocking to 1400W or higher I am guessing this will take much longer. There is no set answer to your question. You just need to be patient until "tuning individual chips" changes to stable for all 3 boards. It could be that your S9s might not work as well with auto-tuning as others have reported here.