Interestingly, this did not fix the issue I was having, however I did find the culprit after some a lot of testing with new projects, and different settings of RMCookTool.
With RMCookTool, you can go to Utilities > Edit Metadata > Essential Information and Presentation, and there is an option to input the 'Game ID', in my case, if it is named ANYTHING that is not 'rmmz-game' it will break the linking paths and cause the whole main.js is missing error.
It seems like this field is fine to leave as default, as when I leave it untouched, the game will launch and function just fine.
