It sounds like your middle coil is running out of phase with the humbucker coils in positions 2 and 4. The wires for the middle coil are wired in the wrong way around in these pictures, try swapping the black and white connections at the switch and the back of the pot. While you have those 2 wires disconnected, measure the resistance between them with a multimeter, that will give you your dc resistance figure to help you to identify the coil.
All of your pickups are mounted the right way around.
When we make single coils, we make the wind direction of the coil and polarity of the magnets correct for their original application, so it may be that you have a middle coil that was originally wound for a full strat set, not HSH. Also, it may not even be a middle coil. In many cases, though, we should be able to get it to work ok once it's identified :-)
If you swap those wires out, pay attention mainly to positions 2 and 4; do you get a fuller signal and do you get lots of hum or very little.
Good luck!