I know little of RC things, being that I just got my first rc thing a month ago (besides a few things like 6-8 years ago)

but I think with your configuration, the motor inside the pvc will suffer problems, as A: the amount of water capable of moving around the motor will be blocked by the motor itself (it convers like 1/3 of the space) which will slow the craft. and, your pvc won't off alot of protection if something gets sucked into the tube, as a peice of plant material would most likely wrap around the prop and the motor housing, 9/10 times severly slowing or stopping the motor.

As for running the wires to the ESC, I think either would work, but if you solder, would rust be a problem?, I think it would be best to insulate all open wire... I'm not sure though...

if anyone out their wants to prove me wrong about this, go ahead, I'm just making guesses