So what is the correct method of calibration? I know F6, U, Y, U, done.
You're doing it correctly.
The biggest variable to accurately bombing that I've seen is varying your speed.
When you calibrate the sight, it's calibrated for the speed you're flying at that moment. If you alter your speed, your bombs will miss. If you calibrate at 160mph, but then allow speed to increase as you maintain level flight, your bombs will hit long. If you slow due to a hard turn, and then drop, your bombs will hit short. If you drop some bombs, and then turn the plane around from the pilots seat for a second pass, (altering your speed in the process) you're not likely to hit anything.
I don't believe altitude matters much, if at all, or whether the ground level changes, because the bombsite angles forward based on speed, which automatically triggers you to drop earlier for a lower target. I could be mistaken there, but it never effected me much.
For best accuracy, climb to your desired altitude, and ideally reach your desired altitude about 1 sector from your target, so you have plenty of time. Once at altitude, you need to allow the plane to settle in to it's cruising speed. Speed will increase in level flight, if you stay at full throttle, and used full throttle to climb. Once you're at altitude, and in level flight, don't steer from the pilots seat anymore. Doing so will generally result in changes of pitch, and steeper-than-desired bank, so will effect your speed. It's much better to limit steering from that point on to using rudder to steer from a gunners position. Open your bomb bay doors, so drag doesn't increase after you calibrate resulting in a shift in speed.
I like to open the E6B and keep an eye on the speed, while steering (with rudder) from the nose gunners position. Once speed has stabilized, which will take a few minutes, you can calibrate. If you do anything to change you speed, you'll need to re-calibrate. I like to calibrate as close to the drop as possible, to eliminate that problem. Enemy fighters can be a problem if you do that, but 90% or more of those can be eliminated by flying right under the cloud layer.
From the nose gunner position, you can also do most of the lining up on the target, so it's just a matter of fine-tuning your aim with the bombsight.
Once you pass your target, if you need to turn around and make another run fly past the target for about 1/4 sector, and turn back using the rudder only, from a gunner position. This will keep your altitude the same. Also, watch the E6B while doing that, so you don't turn tight enough to alter your speed. Your drones will easily stay with you if you do it right.