Feroxhunter - someone is playing tricks with your mind!! I think the only important measure of speed is actual ground speed. Thereafter, you can take any other elements, weather, wind, tide, stream, current into account and adjust your speed to suit your particular style of trolling or lure you're using. If your GPS/fishfinder/chartplotter offers various set-up settings (such as 2D, 3D, WAAS), then set it to WAAS for the greatest accuracy both as to position and speed over ground.
In reality, speed is simply a measure of time over a measured distance. If you really felt that there was a noticable/significant variation between your Luhr Jensen speedo and your gps, which frankly I doubt, then you'd need to more accurately calibrate the log error. No speed log as a measure of speed through the water can be expected to be 100% accurate, as the boat may drag some water along with it, making the water flow past its transducer/impeller/paddlewheel slightly less than than the boat's speed through the water, or the impeller/paddlewheel might not be spinning freely. Alternately, the water flow may be accelerated as it passes the keel or is sucked into the propellor, to make the log overrread. Calibration of any error variance of your gps reading of speed over ground versus your water log speed is of no real relevance to you as a trolling fisherman unless you're trolling from a supertanker!!