Well, that's just lovely.
The FIRST thing I see is IT APPEARS that you have your pots and pup selector switch reversed - pots towards the neck, selector towards the bridge. Is that the case? If you said something about that, I must have missed it or misunderstood you.
If that's how you want the controls laid out, what it means is that you have the 4-way rotated 180 degrees wrong - so when the lever points bridge-way, you the get the neck pup, and vice-verse.
And also, you have the tone pot BETWEEN the volume and the 4-way. That doesn't really change anything, but it sure makes your layout NOT match any of the drawings that I created for you. No wonder you're having novice issues. Bad input = bad output.
If you like that layout, and have enough leads, you should rotate JUST the 4-way so that the common lug with the bridge pup's hot is closest to the tone pot.
If you DON'T have enough leads, do not despair, here's a drawing with the corrected 4-way layout and the volume/tone layout to match the picture you posted of your control plate:
Although NONE of this should affect the issue of the neck being on all the time, you never can tell... Flip the switch OR rewire it as shown, and see if that resolves anything.