maybe this can help...
when I build, I never take reference on the centerline...
I build the body and the neck, then I clamp the neck on top of the body and trace a line onto the body from each side of the neck.
By shifting the neck, I then make sure that both lines are at the exact same distance from the centerline at the very end of the body (of a top for exemple)...
Once its all set, I then take a very small pencil and scribe all around the neck poket aera - this will be the neck pocket which I will then route out...
This technique never failed on me and I get dead on target results as opose to take reference on the centerline and route everything according to that which I used to do before.
the 2 lines i'm talking about here i'm using them to center the pickups for exemple...
PS: dont set the bridge yet, to correct your issue, you could try to shim up the neck pocket and re route it using the technique I just described. If well done you may not even notice the shim because in your case only a tiny bit is required to bring the neck back to the center...