Based on that last photo of the neck, it shows that your neck is a 25.5" scale neck.
That means that the bridge is 0.5" too far forward, being that it sits at 25".
I think you mentioned somewhere that the measurement to the 12th fret was 12.375.
That is to the center of the "fretting" area (Where the dots are).
What you needed to measure, was to the actual fret itself, and that is at 12.75.
To support my theory that bridge is the problem, just look at the pics where you can see the bridge, is it just me or does the bridge seem to be way too far in?
I mean, it looks to be a standard Strat pickguard, and if that's standard, then that bridge is definitely too far forward.
When looking at a Strat with a vintage trem, the saddles barely reach the edge of the pickguard, and these saddles are deep in there...
It may have been a professional job, but me thinks they screwed up........