This paper presents a problem formulation and procedure for design automation of 2.5D interposer-based multi-die ICs. Our approach is designed for (but not limited to) 2.5D ICs that contain one or more dies with flexible I/Os, such as FPGA dies. Given a set of dies, inter-die connections, I/O standard(s) for the connections, and a set of valid die pins for the connections, we simultaneously place dies on an interposer, assign pins to each inter-die connection, and assign specific voltages to I/O bank power supplies of the FPGA dies to produce a valid layout and pin assignments for the design. To our knowledge, this is the first formulation and methodology to consider flexible I/Os in 2.5D design automation. We demonstrate the effectiveness of our procedure through a variety of example 2.5D designs containing different types of interconnected dies.