Include this file into your project and use the Alchitry Cu as another component in you board, easy to use FPGA. It was tested (i.e. manufactured) and dimensions are fine, everything fits:
The connectors you need to buy are "manufactured by" SparkFun and have manufacturer number PRT-16890, I bought them here.
The library includes the schematic symbol
and the PCB footprint
as well as the 3D part for CAD design