I must have searched for hours looking for information to help me with upgrading from the Aqualink RS PDA power control to the new iAqualink. The PDA PCB died and it was a lower cost option to upgrade to iAqualink than to replace. Unfortunately Zodiac doesn't publish publicly the installation manual for the new iAqualink. However the Aqualink RS One Touch install will get you close enough. The newer Zodiac boards come with 2 RS-485 4-pin connectors as opposed to one. All other connectors are the same though they moved to the bottom of the board. The communication cable from the new iAqualink box connects to one of the RS-485 terminals (I used the first one). IF you want to continue using your PDA for On/Off and Monitor functionality you will need to connect the comm cable from the PDA J-Box to the RS-485 terminal as well. You can wire both to the same one.
Now here is the part that I struggled with: getting communication to work with my Sta-Rite IntelliPro VS-3050. The Jandy manual will tell you to wire through a the pump relay.... DO NOT WIRE to the pump relay. The pump should wired directly from the breaker. If you aren't confident in high voltage wiring use an electrician. StaRite and Pentair will tell you to buy an Intellicom II Adapter (a mere $150 "translator") but YOU DON'T NEED it. Page 18 of the Aqualink RS Install Manual, Section 3.3.4 details the pin and wiring configuration needed to connect the Pentair/StaRite control wire to the RS-485 Connector. I used the 2nd RS-485 termination block and connected the Yellow to Pin 2 and Green to Pin 3. With the Intelliflo pump powered on with the breaker you will need to reset the VFD by pushing all 4 Speed buttons simultaneously for 3 to 4 seconds and then power it off via the breaker. This reset step is what I failed to do and it took me hours to troubleshoot.
Follow the iAqualink directions to get it connected to your wifi network. Power up the control board only and allow iAqualink to connect to wifi. All three LED's should be lit. Using the iAqualink Inerface, after you have set up you user account and added your pool, proceed to Menu>System Setup>VSP Setup. Click Pump/Model (#1) and select Intelliflo VS (the flo and pro are the same). If you have a VF I assume this same wiring configuration will work; the difference is you should select Intelliflo VF at this time. Click application and select Filtration. Click Speed Setup>Select your pump>Next - you can now program 8 DIFFERENT speeds with custom labels. You can program to your heart's content. The Jandy Manual for iAqualink is very useful in setting up your system.
Once your system is programmed, power the Intellipro back on via the breaker. It should now operate via the iAqualink.