Make sure the arduino shield does not have any components that could generate a 5V signal on one of the pins.  The FPGA cannot handle this!  I also took away the LED that was connected to pin 13.

Use the arduino shield to connect the SD card reader to the board.  Power (3.3 V) can be drawn from the standard pins.  The SPI pins are also standard for an arduino UNO (pins 10, 11, 12, and 13 are used for SS, MOSI, MISO, CLK respectively).

You can find the file "top.bit" in the "Moncky3_verilog" folder in the project files (https://gitlab.com/big-bat/moncky).  This file can be used to program the FPGA.  Uploading the file to the FPGA can be done with Vivado software (freely available at the Xilinx site).  The chipset of the flash-chip is "s25fl128sxxxxxxx0" and not the one in the documentation of the board.

The assembler will output many different files.  One of them is a ".img" file.  Rename this file to "MONCKYOS".

Now create a partition on an SD card <32 MB (currently only small partitions are supported).  Format the partition with a FAT16 file system.  Now copy the "MONCKYOS" file to the SD card.

Put the SD card into the computer and boot it up.  It should load your project and execute it.