Clarity problems happen when the central conflict gets buried under an avalanche of superfluous ideas.
To enhance clarity in your script, give the reader the thread early. Weight your setup to favor your protagonist and the problem, give less time to secondary characters, set atmosphere with active images instead of conversations.
Keep all of your elements rowing toward the same shore. Make your subplots shadows of the main conflict, which is a shadow of the theme, which is about your protag’s flaw, so that they all reflect and support each other and pay off together instead of charging off in different directions for their resolution.
A script is about one thing, one clear emotional arc. If it is not a structural piece of that arc, it is robbing you of clarity.