First, I would say that those Sleepyhead charts do not indicate any kind of real serious problem with the CPAP setup. You are not having a large number of apnea events with any of the settings. There are some issues with mask leakage on some nights. You have flow limitations and indication of snoring at the lowest pressure setting, but you say that setting gave you the best sleep.
I think I would focus on trying to figure out what is waking you up, and post again on your observations. Ideally one should try for about 7.5 hours of sleep per night to be fully rested for the next day. Waking up once or twice is not all that bad, but no wake ups is obviously good too.
Some comments on your CPAP and setup. You say you have a Resmed S9, but the Sleepyhead reports indicate it is an AirSense 10 AutoSet. I also see that you appear on some nights to be using the Auto Ramp feature that is in the A10, but not in the S9. I'm not real sure your setup is a problem, but if you want to try a new setup and you have the A10 model, here is what I would do. I noted that you know how to get into the Clinical Menu to adjust.
Set the Mode to AutoSet instead of CPAP - That will let you set a minimum and maximum pressure, and the machine will adjust between those limits to give you the minimum needed for treatment.
Set the minimum pressure to 7 cm. Set the maximum pressure to your sleep study recommended 9 cm.
Set the Ramp Time to Auto, and set the Ramp Start Pressure at 7 cm.
Set the EPR Type to Ramp Only.
Set the EPR to 3 (which is where I believe you have it now)
What will this do? First it lets the machine determine how much pressure you need, and it may result in a lower more comfortable pressure (within the limits you set). Using the Auto Ramp Time feature holds at the Start Pressure at 7 cm until it decides you are asleep. I think you may have it at 5 cm now. I find that pressure a bit low to be comfortable and you can feel a bit starved for air while trying to go to sleep. With the EPR set to Ramp Only with a setting of 3, this provides you with maximum comfort while you are going to sleep. Then when you go to sleep it stops the EPR reduction of the exhale pressure. This may also reduce the actual pressure the machine uses to treat your apnea while you are sleeping. Lower pressure not only improves comfort, but it may also reduce mask leaks, which can be annoying too, and wake you up.
So, while I am not sure your machine setup is the real issue, this method of setup could help by improving comfort some. But, most important, try to figure out what is waking you up.
Hope that helps some,