PP's generate tons of heat (those boards are power hogs) thus the reason for the duct and fan. It's not uncommon for that duct to be missing for some reason. The last Pole I did was also missing that duct but still had the fan in place. I wound up making a duct out of some light cardboard (which is all the original duct was). I would suggest you do something similar.
Pole's also had a big tendency to burn up the edge connector due to the high current load on the +5v and ground circuits. That's probably why the edge connector is bypassed. Usually the +5v and ground circuits were jumped directly to the +5v and GND test lugs on the boards. If it looks like a good solid job then I would leave it like that.
Originally PP's were underfused from the factory. There was a bulletin from Atari to up the fuse. I think the original was 15a and it was suggested to up it to 20a, but I could be wrong about the fuse sizes, that was from memory. I have seen problems on the power brick where bad connections at the fuse clips caused the clip to overheat and blew the fuse just from excessive heating of the fuse. You might want to check that.
A couple of other things I would suggest to help improve reliability. First, go over the power brick fully and check for signs of connector heating or thermal stress at the fuse clips and rectifier bridge, very common. Next perform the sense mods to the ARII boards (google for instructions), this helps prevent a board edge connector problem from causing the ARII to drive up the +5v line and roaching the board. Lastly add a fan to the bottom of the cab to circulate air across the brick and ARII boards.
You are lucky you got one with a working board set! It's very common to have board problems and they are a real pain to fix.
Regards,
D