Hey, I just did some checks with the website on which ssl wasn’t working, and everything/ssl is working (with no changes from me) for some reason.
Also, there is now a post on the NFSN forums for an easier, single script to run for setting up Let’s Encrypt. I have gone ahead and swapped over to their script and everything still works. You should give that a try if you didn’t already.
This leads me to suspect CakePHP was not the problem here, even though I was led here from NSFN forums saying it doesn’t concern let’s encrypt :d. Not sure why it works now but I don’t want to spend time figuring it out right now, I’ll leave it be since it works!
Let me know if the “new” script gets it going for you. Best wishes.