I tested the windows distribution on your website which seems to perhaps be your 2004 build, and the integrated workflow for converting wav files to gsm is great. It also includes a good tool for concatenating files.
When building from the new source code, I found that the easiest way to create GSM files was to just use the old windows distribution's Go.bat script.
When it came to concatenating the .GBFS file with the GBA rom, the suggested command on Windows wasn't working for me. I'm used to Linux and macOS where this is easy to do. However the included bin concat command in your old windows distribution did the job perfectly,
Anyway, it could be worth distributing those tools with the newer source code, or else pointing users in that direction for these steps.