This is really nothing more than a simple drafting problem.
Take a look at the attached JPEG where I have tried to illustrate my previous post. When you did your measurements, if the pendulum was swinging in a plane that is not parallel to the picture plane (the plane that projected against to track its motion), then it will be marked out as an ellipse. On the left is the desired picture. At the top left is a horizontal line representing the top view looking down on the swinging pendulum which marks out a straight line. If we project this down to the picture plane (the long horizontal line) and then draw out the front view, the pendulum will move in a perfect circular arc. Now let us rotate the pendulum's plane of oscillation to be at an angle with the picture plane, which is drawn on the right. At the top right you see that the pendulum is now swinging at an angle but it still marks out a path of the same length. If we project this down to the picture plane and draw the front view, we have three points of reference for the vertical positions. We know the two points at the ends of the pendulum path are the apex of the swing and the middle point is the lowest point of the swing. So we project these over and find the intersections. The dased line shows a circular arc made from the apex of the swing but the actual path is shown by the solid line, which is elliptical.
Thus, if the pendulum is swinging at an angle to how you are projecting it when you map out the path, then it will appear elliptical. You can correct this by having a second map that is normal to the picture plane (a side view or the top view like I have shown) and using these two views you can reproduce the desired projection on the left in a process that is basically the opposite of what I explained above.
As for your question about the angle, it is obvious from our image that the since the angle is dependent upon the horizontal position of the pendulum's apex, then the angle will be incorrect. It will be smaller than the actual angle.
EDIT: I should make the caveat that the actual elliptical path shown in the picture is probably not the actual one since it was produced by only the projection of three points. Really what you would do is you would project a large number of points, maybe 15 or so, and use a spline curve algorithm (or plain old french curve by hand) to interpolate the elliptical path that the pendulum follows. What I mean is, I am not sure if the actual distorted path is a perfect ellipse, it may be even more messed up than that but it is a decent first order approximation because we can at least see that the circle can only satisfy at most two points.