There is a gap on one side of the neck (shown before)...
That gap on on the treble side of the fretboard does look a bit excessive but the "overhang" of the fb is not meant be joined to the body on that style of guitar. The mortise and tenon are the contact (glued) points of the joint and they're off-centre creating that overhang.
As long as the bottom (and sides) of the heel (tenon) are respectively flat and tight in the pocket (mortise) then there should be no problem. (I don't recall a photo of that part of the joint)

...and the whole fret board seems pretty high when the neck is in place...I measured it at 15mm from the body to the fret board.
I have not built an ES kit, but guitars that use a TOM (Tune-o-matic) style bridge and ring-mounted humbuckers tend to have the fretboard a bit higher, than say a strat or tele, in relation to the body to clear the height of the elevated pickups and accommodate the bridge height.

My set-neck and LP-style guitars all sit about 11mm from the body to the centre of the fretboard radius, so 15 may not be that extreme. Again, I have no personal experience with the ES kits.

I’ve noticed that the volume and tone pots are the wrong way round compared to PBG advice (A = volume B = tone) does this matter?
Yes, and no. Electronically speaking one or the other are not right or wrong. They will each do the job, albeit slightly differently, but convention is A volume; B tone. It's more personal preference and how a player uses (and hears) the controls.

I've recently started using A (audio/logarithmic) pots for both volume and tone, but I have plenty of guitars that are A volume, B tone. I've had lots of import guitars on my bench that have the reverse like yours and I just leave them unless instructed otherwise.

I also think I’ve found another stumbling block...the wire from the P/Up selector to output isn’t long enough to reach...any ideas on what to do?
Sorry to sound like a smart-arse but, solder on a longer wire...