When you say cooking to my mods folder, are you filling in the shootergame/content/mods in the cook dialog?
the cook process produces a mod 123456789 folder and real content in a separate ‘modname’ folder together with a 123456789.mod file. A different layout than a normally installed mod.
I have not got direct to content folder cooking to work reliably. While developing locally, I cook to another folder then copy the content of the cooked ‘modname’ folder over my previously installed mod content the numbered folder in the game mod folder. I use ‘beyond compare’ to identify the changed files. But this does rely on having done a steam upload and install at least once!
Hope this helps!