In this paper we describe a flexible infrastructure that can directly interface unmodified application executables with FPGA hardware acceleration IP in order to 1), facilitate faster computer architecture simulation, and 2), to prototype microarchitecture or accelerator IP. Dynamic binary modification tool plugins are directly interfaced to the application under evaluation via flexible software interfaces provided by a userspace hardware control library that also manages access to a parameterised Bluespec IP library. We demonstrate the potential of our infrastructure with two use cases with unmodified application executables where, 1), an executable is dynamically instrumented to generate load/store and program counter events that are sent to FPGA hardware accelerated in-order microarchitecture pipeline, and memory hierarchy models, and 2), the design of a branch predictor is prototyped using an FPGA. The key features of our infrastructure are the ability to instrument at instruction level granularity, to code exclusively at the user level, and to dynamically discover and use available hardware models at run time, thus, we enable software developers to rapidly investigate and evaluate parameterised Bluespec microarchitecture and accelerator IP models. We present a comparison between our system and GEM5, the industry standard ARM architecture simulator, to demonstrate accuracy and relative performance; even though our system is implemented on an Xilinx Zynq 7000 FPGA board with tightly coupled FPGA and ARM Cortex A9 processors, it outperforms GEM5 running on a Xeon with 32GBs of RAM (400x vs 700x slowdown over native execution).