Even if $sin$ and $cos$ are not the right basis functions, you can still expand $f(x,y)$ as $f(x,y)=\sum_{n}C_{n}(x)e^{iny}$, just as an example.
Then you can plug such a representation into an equation and you'll get an ugly mess, but sometimes you get lucky and the equations have a resonable form for at least getting an approximate $C_{n}$.
This is the hope if the $e^{inx}$ are somehow related to the equation in $x$.
That's what I am suggesting here, but with the eigenfunctions of the modified periodic condition.
The eigenfunctions you found when plugged into the original equation will give an eigenvalue times the eigenfunction but with a left-over term.