Okay, here goes nothing:
1) Since you bought a dual pick up rudder, you will need to run a second water line through the transom. I would copy what's already there, thus keeping it simple
2) Run one of the water lines to the motor, the other to the ESC. If you want to put in a "Y" fitting, you can, running one line to each side of the ESC and each end of the motor
3) Next to the existing outlet on the left side of the boat(that area is called the nontrip, just an FYI) drill a second hole and install the drain fitting into it
4) Run your water drain lines to the fittings through the left side of the boat. IF you split the intake lines, install a second "Y" fitting into the drain lines so you can use just the two fittings
5) Swap out the ESC with a heavier version that can handle higher voltage and current, be sure you use no smaller than 12 guage wiring and keep the wires short
Since you want to run larger battery packs and ESC, you will need to rebalance the boat. You want it to balance right about where the turn fin is located. Too much further forward and the boat will try to submarine on you, too far back and it will try to fly.
As far as why I said to install the drain fitting next to the one already in the boat, it's to make sure you're getting water flow through the cooling system. To put in on the right side will make it impossible to see the water coming out, not a good thing since the water going through the cooling system is all that will keep the motor and ESC from overheating.
Stick with the stock drive train for now. Once you get everything else reworked and tested, you can go with a larger cable and prop if you wish. Word of caution, too much prop or too much cable drag will overload the batteries, ESC and/or motor.
I know some will tell you to put a water pick up through the hull bottom, DON'T DO IT!!!!!!!!!!! If the boat is running properly, a through bottom pick up won't do any good since it will be constantly above the water