This is how to do it:
Go to bombsight view.
Open your map, hit U, click on area you plan to bomb.
Close map. You'll see the target alt has probably changed from 0. Could be 1k, could be 182 feet, depends on where you clicked on the map.
Now pick a spot on the ground, and use your joystick to put the big crosshairs on it.
Hold Y, while keeping the crosshairs on this spot using your joystick.
The longer you hold Y, and more accurate you are holding the cross-hairs in place, the better accuracy you will have.
When you release Y, you'll see your calibrated speed has changed. You can check this against your E6B true air speed. If they match, bombs will be on target. If your calibrate speed is higher or lower, the bombs will go short or long respectively.
It's very, very easy once you've done it correctly.
If you still end up with a speed of 3625, you moved the crosshairs way too fast, and not on your reference point, during calibration