So, to clarify, for anyone else who finds this post. What I was doing incorrectly was that was using Tasks > build > build but I was taking the .jar file from my /build/libs folder, which is named after my modid (so in my case it's named justfileapi-1.0.jar), but this is a pre-re-obfuscated version of the jar. In the /builds/reobfJar/ folder however there is an "output.jar" file which is my re-obfuscated .jar file -- this is the final version which I manually renamed and deployed.