a friend asked me this question; after a bit of searching, I'm still unable to answer it.
Question Are there two rings with isomorphic centers which are not Morita equivalent?
Our first method of attack was to use that Morita equivalent rings have isomorphic $K_0,K_1,$ and $K_2$. However, Bass proved in '64 that f.g. projective modules over the monoid ring (over a PID) on a free monoid are free, so $K_0$ doesn't distinguish $F\langle x,y\rangle$ from $F$. I know that $K_1(F)$ is the units of $F$, but I'm having a hard time finding any computations of the $K$-theory of noncommutative rings like $F\langle x,y\rangle$.
It would be awesome if there was a counter-example proved using low degree $K$-theory, but any counter-example would work (assuming one exists).
Let $k$ be a field with nontrivial Brauer group, and let $A$ be a central simple algebra over $k$ representing a nonzero class in its Brauer group. Then $k$ and $A$ are not Morita equivalent, but both have center $k$. For example you can take $k = \mathbb{R}, A = \mathbb{H}$.