I originally asked this in an answer to the following question:
What is the equation of an ellipse that is not aligned with the axis?.
As I noted in the opening paragraph I DO NOT HAVE THE NECESSARY REPUTATION TO COMMENT YET. That was why I had to provide an answer rather than doing the very natural thing of commenting.
Two people: pjs36 and Ben S both advised asking a new question, even though I believe this is a duplicate of that question.
The problem is very simple: user1089161's answer is almost a perfect answer for the problem I'm trying to solve, except it is expressed in terms of the slope 's' along which the major axis lies. This means that if the major axis is parallel to the y axis, the answer becomes degenerate.
So how could that answer be expressed in terms of the angle by which the major axis has been rotated rather than the slope on which it lies?
Copy & paste from user1089161's answer mentioned for reference: $$\frac{((y - y_c) - s(x - x_c))^2}{m^2(1 + s^2)} + \frac{(s(y - y_c) + (x - x_c))^2}{M^2(1 + s^2)} = 1$$
Let use replace $s$ with $tan\theta=\frac{\sin\theta}{\cos\theta}$ to give:
$$\frac{((y - y_c) - \frac{\sin\theta}{\cos\theta}(x - x_c))^2}{m^2(1 + \left(\frac{\sin\theta}{\cos\theta}\right)^2)} + \frac{(\frac{\sin\theta}{\cos\theta}(y - y_c) + (x - x_c))^2}{M^2(1 + \left(\frac{\sin\theta}{\cos\theta}\right)^2)} = 1$$
Next multiple each fraction by $\frac{\cos^2\theta}{\cos^2\theta}$. Note the denominators then include a $\cos^2\theta+\sin^2\theta$ term which disappears.
$$\frac{(\cos\theta(y - y_c) - \sin\theta(x - x_c))^2}{m^2} + \frac{(\sin\theta(y - y_c) + \cos\theta(x - x_c))^2}{M^2} = 1$$
This answer can also be arrived at from Américo Tavares' comment to Henry's answer in the mentioned question. They use a matrices based approach. I don't know your background so you may not have yet covered matrices but an application of matrices is finding rotations/reflections/other transformations of 2D (or higher) shapes.