Reconfigurable devices are often employed in heterogeneous systems due to their low power and parallel processing advantages. An important usability requirement is the support of a homogeneous programming interface. Nevertheless, homogeneous programming interfaces do not eliminate the need for code tweaking to enable efficient mapping of the computation across heterogeneous architectures. In this work we propose a code optimization framework which analyzes and restructures CUDA kernels that are optimized for GPU devices in order to facilitate synthesis of high-throughput custom accelerators on FPGAs. The proposed framework enables efficient performance porting without manual code tweaking or annotation by the user. A hierarchical region graph in tandem with code motions and graph coloring of array variables is employed to restructure the kernel for high throughput execution on FP- GAs.