I've found the best tool for getting certs from LE is this:
It also unconditionally tries to listen on ports 80, 402, 443, 552 and 4402 whenever it completes a challenge, even if you have absolutely no intention of using any of these verification methods, so there's a lot of moving parts most of which you don't want.
I made a FreeBSD port, but thought twice about submitting it: https://github.com/Freaky/ports/tree/master/security/acmetoo...
It is weird that it attempts to listen on all of those ports, though.