I had the same issue with mine
used a caliper for verifying it
I will not get into how disappointed I had been with the system for the first week of trying to work out why every thing was blunt when I got onto the slicing table
I also noticed different stone kits had different thickness’s that changed the angles a bit
so I had no choice but to re burr for every grit I changed over to
until I made a micro angle adjustment that I use to recalibrate each stone with
much like what you have finally came up with along with your new ball joint design
mods
1st being gluing down the main jaw
( seriously aluminum is no good for screwing things into its just to soft )
2nd adding spring to the angle adjustment screws
( kept coming loose after about 20 pass’s )
3rd making longer thicker rods with ball joints and having protective boot
( to much play in the rods and jig was useless for larger knifes ie. machetes )
4th making new jaws
(same height just not aluminum so they are stronger and thinner allowing lower angles)
/
new base as the angles where not asymmetrical aluminum might have stretched or drilled in wrong spots?
5th finalizing making micro adjustment as the different stones were throwing angle off
( our ball joint system sits on a rack and pinion system that is adjusted by a worm gear )
6th making another knife holder steadying pole with clamp and height adjustment
the original pole was higher then the level of the knife keys and gap was to shallow for any of my knifes to even for their tip to go into
its hard getting dad to build something that you want until you waste a heap of money on something that needs improving … he likes his KISS theory to much
so far with all the modifications we have almost rebuilt the entire jig in fact the only part that is still being used is the angle bar because math hurts my head to much 
all in all love the WEPS more then my edge pro even tho its been completely remade apart from the stones