The tail lamp harness will easily clear the cover.
Here are two photos from a different 42WLA. It is on the lift right now having its rebuilt engine installed. The taillamp harness is in basically the same location as in the WLA above's photos.
When I run a harness (this also applies to control cables), I will lay it out on the frame loosely and mount one tank and check the clearance. I will then take that tank off and mount the other side and reverify that all the harnesses and controls clear properly.
Sometimes, when I am dealing with a setup I am not familiar with, setting only one tank on will reveal the routing locations that H-D intends to be used.
I also do this to verify that the tank itself is fitting properly on the frame (touching only at the mounts and not rocking between mounts). If necessary, I will add a 0214 washer between the tank and frame to give it the right clearance. I might also do this if the tank is pinching the harness and the harness is in its right spot.
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