Currently the Plot class is littered with strange Lists and LINQ queries to manage axes. Try to wrap this complexity inside a helper class like an AxisManager or something. It should manage the axes in lists contained inside it and provide helper methods for easily adding multiple axes.

Do something similar with the grid system since there can be multiple grids.

This is really big breaking API change... ScottPlot 5 is marked as a preview package with warnings that the API is evolving, but I see this potentially affecting a lot of people.