Tomorrow will mark the week long duration of this issue. Please do read the information provided, we have all taken time to provide what we can (while respecting customer privacy etc).
Good information exists here, with an endpoint Let's Encrypt staff can test against. Here: "your server may be slow or overloaded" acme-v02.api - #16 by jc-rimu
I will re-assert: The MTU workaround is NOT a fix.
For the Let's Encrypt team: we do appreciate your steps towards identification/fix.