Your problem is that you add an additional ##r## in your surface element. This is presumably because you think that in polar coordinates you need to use ##r\,dr\,d\theta## for the area element, but the ##r## is already accounted for in the cross product ##\vec r_r \times \vec r_\theta##. (Consider the flux of ##\hat j## through ##y=0## and ##x^2+z^2 \leq 1##, which should clearly be -up to a sign depending on normal direction- ##\int r \, dr\, d\theta## over the same ranges of ##r## and ##\theta## as you have.)
Generally, the surface element as parametrized by ##t## and ##s## is given by
$$
d\vec S = \vec r_t \times \vec r_s \, dt\, ds
$$