The information in the howto on https://wiki.geany.org/howtos/win32/msys2 were pretty old and also partly outdated. Some months ago, I started to rewrite the howto to be more accurate and recent. It took some time but I could finally finish it (except the release.py scripts, I forgot to copy them from my Windows machine, will do in a few days).
The updated howto now also uses `osslsigncode` for code signing which is easier to install and use than the Microsoft SignCode tool.
Some remarks regarding your mentioned problems above: - it's way easier to do anything regarding compilation and installation from *within* a MSYS2 shell - using the native Windows command prompt is not been tested and supported and probably makes things just more complicated - the release scripts and especially the code signing is not important for you, these steps are only necessary if you would build a full binary release for distribution but for local development I recommend to skip these steps