I think I've solved this. By replacing A
θ with A
θ/R and using the spatial curl operator defined below for the magnetic fields it works out correctly. The curl is the spatial ( and temporal ) parts of F_{\mu\nu}=\partial_\mu A_\nu-\partial_\nu A_\mu.
The curl operator in cylindrical coords is equation (117) on this page
http://mathworld.wolfram.com/CylindricalCoordinates.html
So far I've done the calculation on a piece of paper and it gives the right contraction but I'll set up a script when I can to check it. As I said earlier, the differential operators must be correct for the coordinates used.
[added later]
Using equation (117) the magnetic fields are
<br />
\begin{align}<br />
B_R &= \frac{1}{R}\frac{\partial A_z}{\partial \theta}-\frac{1}{R}\frac{\partial A_\theta}{ \partial Z}\\<br />
B_\theta &= \frac{\partial A_R}{\partial z}-\frac{\partial A_z}{ \partial R}\\<br />
B_Z &= \frac{1}{R} \left[ \frac{\partial A_\theta}{\partial r}-\frac{\partial A_Z}{ \partial \theta} \right]<br />
\end{align}<br />
and the electric fields are
<br />
\begin{align}<br />
E_\theta &= \frac{1}{R} \left[\frac{\partial A_\theta}{\partial t}-\frac{\partial A_t}{ \partial \theta} \right]\\<br />
E_R &=\frac{\partial A_R}{\partial t}-\frac{\partial A_t}{ \partial R}\\<br />
E_Z &=\frac{\partial A_Z}{\partial t}-\frac{\partial A_t}{ \partial Z}<br />
\end{align}<br />
now we can write
<br />
F^{\mu\nu}=<br />
\left[ \begin{array}{cccc}<br />
0 & \frac{\partial}{\partial\,t}\,A_R-\frac{\partial}{\partial\,R}\,A_t & \frac{\frac{\partial}{\partial\,t}\,A_\theta-\frac{\partial}{\partial\,\theta}\,A_t}{R} & \frac{\partial}{\partial\,t}\,A_z-\frac{\partial}{\partial\,z}\,A_t\\<br />
\frac{\partial}{\partial\,R}\,A_t-\frac{\partial}{\partial\,t}\,A_R & 0 & \frac{\frac{\partial}{\partial\,R}\,A_\theta-\frac{\partial}{\partial\,\theta}\,A_R}{R} & \frac{\partial}{\partial\,R}\,A_z-\frac{\partial}{\partial\,z}\,A_R\\<br />
\frac{\frac{\partial}{\partial\,\theta}\,A_t-\frac{\partial}{\partial\,t}\,A_\theta}{R} & \frac{\frac{\partial}{\partial\,\theta}\,A_R-\frac{\partial}{\partial\,R}\,A_\theta}{R} & 0 & \frac{\frac{\partial}{\partial\,\theta}\,A_z-\frac{\partial}{\partial\,z}\,A_\theta}{R}\\<br />
\frac{\partial}{\partial\,z}\,A_t-\frac{\partial}{\partial\,t}\,A_z & \frac{\partial}{\partial\,z}\,A_R-\frac{\partial}{\partial\,R}\,A_z & \frac{\frac{\partial}{\partial\,z}\,A_\theta-\frac{\partial}{\partial\,\theta}\,A_z}{R} & 0<br />
\end{array} \right]<br />
and (finally ?) g_{ma}g_{bn}F^{ab}F^{mn}= 2(-E^2+B^2) where g_{mn}=diag(-1,1,R^2,1).