Rewrite the whole thing in HTML and JavaScript and stick it in an iframe.
An example of a recent article that's done this well is SCP-3340. Check the source on that one to get a feel for how Dr Aers did it.
The gimmick used in 3340 revolves around doing stuff when the user refreshes the page, which is fairly easy to detect in JS. SCP-2505 - which I think is the one you mention in your OP - is considerably more complex. The idea that you propose is somewhere between the two, in terms of difficulty (but that's coming from someone who hasn't tried it, and it's always more complicated once you get into it).
A couple of ideas for how you might achieve your proposal:
- You could prepare several different versions of your document, each one more incoherent than the last, and replace the entire article with them after each ~30 seconds, maybe.
- You could randomly select individual letters in the article and change one into a random letter every second or so.
- You could detect the reader's scroll position, and make your article more incoherent based on that.
Overall: this is very possible, but if you don't already have a solid understanding of HTML and JavaScript, you're going to have a tough time.
If you want to learn them or want to brush up (sorry, I don't know if you know any JS), I'll recommend Codecademy as a good place to start, as that's where I started learning JS myself. I can't teach you, but if you want to shoot me a few questions about how to do stuff, let me know.