There are 2 categories of rocker geo in this.
#1 is the stuff you have to live with, which includes the cross-wise pushrod angle due to overhang, the fact that the tappet centers are different from the rocker centers on the same cylinder, and the lengthwise (crank rotational axis) pushrod alignment. You can make it better, but it's still there.
#2 is things that can be erased and made to function normally, specifically the geometry at the rocker itself.
To get the long (valve-side) lever in the right place, you have to seat one valve and place the roller tip on the stem end, then open the valve to mid-lift (lobe height × 1.23 rocker ratio × 50%).
Normally, the choice of what percentage of lift to reach by 90° is between 3 alternatives:
1. Miller's "mid-lift" method [lever positions at start & finish are equally above & below horizontal]- 1/2 lift (largest area)
2. high-pivot Jesel/Johnson/Titan method [lever starts pointing too close to horizontal, ends pointing too far down] - roughly 1/3 lift (faster opening, slightly less total area)
3. low-pivot reduced thrust load method [lever starts pointing too far up, ends pointing closer to horizontal] - roughly 2/3 lift (lower guide thrust at high spring load, slightly less area, and timed too late)
In H-D engines, I would not use anything but 50% because the tappet offset already makes tappet motion BTDC faster than ATDC, and any more change makes me nervous.
To do this, a line through the shaft center and the roller axle should now be at 90° to the valve stem. Your jig appears to use the contact point of the lever, which is error with a roller, and places the lever's effective end 50% of the roller diameter too high (typically 3/16").
If the angle is off, try to measure it using trig and at least get the same angle for the same valve on the other cylinder. If the angle has passed 90°, it's not too bad. Not reaching 90° must be fixed.
The correction is to move the shaft up or down, very difficult with a knuck (and moves both rocker the same amount). Since the box position is fixed in 2 places (both the shaft centers and the casting thickness), the box can be moved on the horizontal ears easily (shim up or machine down), but moving the shafts in the vertical ears requires welding, offset bushing, eccentric adjuster, etc. Much easier to add a lash cap, or change the valve length (and perhaps the spring).
To get the short (pushrod-side) lever in the right place, you have to clock the lever's socket end to align with the tappet (which is raised to 50% of lobe height), and this is where all 4 levers will differ.
Yes, the pushrod will still have a dog-leg, because the tappet itself is still at 22.5° to vertical (rather than clocked to aim at the rocker, as the knuck was designed).
PLEASE: do not take this as instruction for any other engine, even another knuck. This one has special features, and a pan or shovel is even more different.