i always put a center mark on material when carving a guitar body if material is 26 inches wide I put a line at 13 inches when homing the bit where do you place it so that the guide 1/4 hole Hits right on the line I placed.
If i am understanding correctly, you want the guide hole for 2 sided carving to hit your center line, this would be done in whatever Cam software you are using be it Easel or Vetric, etc.
lay out your guitar body then set a couple drill toolpaths,
what is happening is Im setting my home/zero on the lower left corner of the material im using I do have the guide hole placed at 12 inches on a 24 in piece of material in the design when it routes that guide hole it misses the centerline everytime always to the left of the line. im assuming my zero mark isnt correct or im not placing the home position correctly
or you didnt calibrate your X steps, so you may not be getting full movement.
There are some good videos on site on how to calibrate your axis’s