In this paper, we introduce the Woolcano reconfigurable processor architecture. The architecture is based on the Xilinx Virtex-4 FX FPGA and leverages the Auxiliary Processing Unit (APU) as well as the partial reconfiguration capabilities to provide dynamically reconfigurable custom instructions. We also present a hardware tool flow that automatically translates software functions into custom instructions and a software tool flow that creates binaries using these instructions. While previous research on processors with reconfigurable functional units has been performed predominantly with simulation, the Woolcano architecture allows for exploring dynamic instruction set extension with commercially available hardware. Finally, we present a case study demonstrating a custom floating-point instruction generated with our approach, which achieves a 40x speedup over software-emulated floating-point operations and a 21% speedup over the Xilinx hardware floating-point unit.