The first thing I needed to do was rather simple. I had to look at the difference between story and plot. Story is rather simple. John and Mary meet. They get married. That's a story. The heroine escapes from her evil wizard father. She finds a man who makes her feel worthy. That also is a story.
So what is plot. John and Mary meet. They marry. She learns he is having an affair. That's a plot. Or in my case. The heroine escapes from her evil wizard father. She finds a man who makes her feel worthy. Then she learns the wizard threatens her new found happiness and also her new home. There is the seeds of the plot.
Remember this. A plot is just a plan. A gradual unfolding of a series of motivated incidents.
Essentially, there are three basic plots and hundreds of variations on these themes. Man against man. Man against nature. Man against himself.
So if you find holes in your plot, look at these elements. You can use one and have the others as subplots. Or just one element alone and turn your story into a plot.