Recommendation? How Long to Burr when Reprofiling

Use a Sharpie often and switch to diamonds.
If using a vitreous stone, make sure it is flat and not glazed or plugged. It can take a few on a full size bench stone, so on a smaller stone you'll need some patience.

Sight down the edge and check if it is off center, might as well correct any oddities at the same time.

Not familiar with using an Edge Pro, but make sure the blade isn't moving around.
 
Be sure to compensate for the grind of your knife when measuring your angle using your Edge pro.

Depending on the knife, when you lie it flat on the edge pro table on the face of your grind then you're effectively sharpening at a much lower angle than you're measuring. Possibly even 5 degrees lower.

Level the angle cube on the edge pro table, then place your blade on it and measure the grind of your blade with your angle cube. Use half of this measured angle to get the mid-point of your grind angle then subtract that from your sharpening angle that you measure with your stone in the clamps and resting on your knife. This will be your true sharpening angle.
 
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