The Gotek is in place and the ST back together. The Flash Floppy firmware (0.9.9a) is installed.
The next small challenge was trying to figure out what the correct files to install on the USB drive. There is a helpful thread here written by a user named rubber_jonnie with instructions to setup a Gotek on the Atari ST.
The thread takes you step by step on installing the firmware and setting up the USB. A definite read for first timers.