I totally get what you are saying, sorry for taking you too literally about your codepen example :)
As the main compexitites in the javascript are jQuery itself, thats where most of the organisation is, you are then tapping in to that library of possible functions etc.... If you were doing all the jQ stuff yourself youd find that much easier to organise (there are lots of logical groupings).....
..... but .....
As you are just using some bits of jQuery you have two main options.
Logically group your functions together and comment them well - you'll end up with basically a headed list of groups of functions/lines in your file.... (although I imagine this is where you are already)
Go more OO, group funcs by creating objects that hold functions..
'logical gouping' could be taken many ways - but how about 'all these function contirbute to the specific functions of this page , or group of pages', or 'all these functions go together to make this modular element complete' - A happy side affect of this is you should end up with modules of code that contirbute specific functionality, that you can probably use elsewhere in your projects for free. (see Mr. Petrov's answer)