Guidelines for measuring a standard "sill" type rectangular window opening

Window must be measured in at least three locations both vertically and horizontally.

Diagonals must be measured and compared. If the two diagonals are not the same this means the window is "skewed".

A straight edge must be used to ensure all window sills are straight.

A square must be used to ensure all corners are truly square:

Measure the clear glass surface inside any molding or channel. Make sure all molding / channel widths are close to the same. This helps me ensure there is no "shadow" on the stained glass window from the molding / channel.

Does the window frame have anything which could prevent a rectangular stained glass panel fitting inside the frame? Exposed latches or hinges? Bumps? Rounded corners? Anything else?

Measure the depth of the sill.