2) I assume the coords in the file relate to placement, but I don't know exactly how. Maybe place three tractors of different types in an L shape and then check the file and compare numbers, so you can learn which why the grid #s mean - and use that to find your beehive.
2) or you can just look for the beehive using the overhead -- click the Sell button on beehives and just move the cursor to pan the camera around til you find it.
3) Once you find the beehive you want to sell, after clicking the Sell button - click the beehive from the overhead view and it will be gone. Much the same as clicking a spot on the Buy overhead placed it there.