EDIT: can you post a pic of the wires soldered to the Wii as well?
I'm leaning towards it possibly being your wire pairs going to CM1/CM2 on the Wii board.
I'd recommend tightening the twisting on those wires a bit more. It's very crucial that the twisted pairs be as tight as possible to avoid noise on the line.
If you have a drill, or Dremel/rotary tool you can stick two wires into it with a tool bit and use it to twist your wires SUPER TIGHT. Then separate them and tin them for soldering to the board.
As for the external ports on the Wii board you're using;
Did you sand the edges of that donor board and check for shorts after you cut it? I think I see some copper laying over the top of the board.
That could be causing a short between any of the layers, and preventing the drive from booting properly.
As for drive location. The row of pins in the rear (farthest from where the drive is inserted) is for the bottom port and the second row (closest to where the drive is inserted) is for the top port.
Here is how I have my external bench tester set up for reference.