Lets see if i can break this down.
Fan speed control is based on the system SDR file which needs to be loaded and configured before any fans speed control is enabled. Most systems using the S5500WB have 4 fans. 2 CPU and 2 memory. Sounds like yours onlys has 3 fans? You need to know which are connected as the SDR loading tool will ask about each fan (if you select "other")
Yes - SSI Front panal connector ( J1E2) pin 20 is the chassis signal line.PIN 13 & 17 are GND. I don't recall if it is requires an active high or active low. I believe low to indicate a chassis intrusion.
There is an option for a front panel temp sensor, but it is not required for fan speed control