The emonPi you’re going to buy How open is my data? Can I download or record it into, say, Google Drive? is designed for the normal domestic UK single phase supply.
The emonPi can only measure the voltage of one phase, and only calculate real power on one phase. So you’ll get wrong answers if you put a c.t. on the second phase. What you propose won’t work.
For what you want, I’d recommend an emonTx with the 3-phase PLL software (to upload that onto an emonTx to replace the default software, you’ll need a programmer from the shop) and an emonBase instead of the emonPi.
You’ll then have 4 c.t. inputs (one is more sensitive low-current), each of which you can allocate to whichever phase you choose. Because, like the emonPi, the emonTx has only one voltage input, it relies on all phase voltages being the same as the one it’s measuring. If the second phase voltage is significantly different, that’s a source of error. You can still have the optical pulse sensor on you generation meter, or you can have a c.t. or both.
I’ve already explained that your data is stored on the emonBase - because an emonBase is an emonPi without the analogue energy measuring part - so you store it “online” as well.
We have instructions for setting up the Arduino IDE that you’ll need to change the software on the emonTx in the ‘Learn’ section, you can look at those and download the sketch from Github to see the sort of stuff you’ll be handling. I presume you’re OK with editing text files, saving them, etc, and typing console commands?