3. The distance between pickup and string is a very important factor for output and sound.
As a general rule for a starting point:
For the bridge pickup - put a nickel on top of the pickup under the high E string and play the highest note on that string. Adjust the height on that side of the pickup till the string touches the nickel. Repeat the same with the low E string, but use two nickels on top of each other. If this gives you too much output, you can reduce the height slightly. Don't forget that twice the distance will reduce the output by about 60%, and the sound will lose some lows. NOW, you can adjust the neck pickup to match the output of the bridge pickup. For the sound test, use stage volume.
4. The position of a pickup is the key for the tonal response between lows and highs.
One of the main flaws of multi-pickup guitars is the difference in sound between bridge and neck pickup. If you adjust your amp to get the right sound from the bridge pickup, your neck pickup might sound too bassy; or it's the other way around when you adjust the amp that the neck pickup sounds right. Also, a pickup in the neck position generates a much stronger signal than the same pickup in the bridge position. This is caused by the amplitude of a vibrating string which reaches, normally, its maximum at the center of its speaking length.
5. The position and the angle of the attack is where You, the player, takes over.
Experienced players can create all kinds of sounds, just with their right hand technique. About a year ago, I was playing at a blues jam, and during the break, a young player asked me, "How do you switch so fast from the bridge pickup to the neck pickup, sometimes in the middle of a fast phrase?" I told him, " I don't", and showed him my guitar. He couldn't believe it, my guitar had only one pickup - the neck pickup. I told him all about the hot and the sweet spots on a string.
Try for yourself -- take your guitar and switch to the neck pickup and set your amp on low volume. Pluck your string with a medium thick pick at a right angle with medium force. Start to pluck the string at the end of the fingerboard, and, slowly, go up towards the bridge. You will recognize a steady change in output and tone, and somewhere close to the center between bridge and neck, you will find that beautiful sweet spot. Now, change to a more forceful attack, and also change the angle of attack to 45 degrees; you'll be surprised of all the sounds you can get! Then, repeat the whole process with different pickup selections. Single coil pickups are generally more sensitive to these changes than large humbuckers. It requires a lot of practice before you can master this technique, but with practice, you can duplicate the effects of a wah wah pedal just by changing the force, the position and the angle of the attack.