ok..... I will now make it this as clear as I can.

"Now you're weeping shades of cozened indigo
(Musta) got lemon juice up in your eye"

Yes, indigo is referring to the third eye chakra in the song. Now, hes not talking about the opened third eye, Maynard is talking about the out of balanced or shaded thrid eye.

The third eye is the center for intuitive perception, vision, dreams, imagination, concentration, intellect, etc.

When the third eye chakra is out of balance it causes you to be judgemental, fearful, gossipy, etc.

This seems to be the dark or shaded aspect of the third eye chakra. It is also known that when people ignore their shadow side they tend to be a hypocrite. This is because they hide in the fact that they to have issues and problems so they must play innocent by crying out that a specific person is guilty when clearly they are guilty as well. Therefore they are weeping shades of cozened indigo.

This part is only a thought:

Obviously lemon juice in your eye would cause you to cry. Maynard is talking about the third eye. I have a thought on the lemon juice, but I'm not so for sure I'm right. All I know is that the lemon is yellow and so is the will/ego chakra. So maybe the ego could be getting in the way of the third eye functioning properly. yellow is opposite to indigo on the colour wheel.