LetsEncrypt is a tool that simply generates certs and keys. Some of the magic is in the clients that can auto regenerate when certs expire but there is nothing stopping you from doing it yourself by hand. Be aware though that LetsEncrypt issues certs that expire in 90 days so you will have to repeat this process frequently until Modulus supports a client.
Install LetsEncrypt
$ git clone https://github.com/letsencrypt/letsencrypt
$ cd letsencrypt
$ ./letsencrypt-auto
Note: At the time of this writing Mac OS X support is very experimental. To ensure this installs correctly you may want to use a Linux distro
Generate SSL Cert:
$ ./letsencrypt-auto certonly --standalone -d example.com
Copy into modulus admin
# pbcopy is a Linux command that will copy the contents of a file to your clipboard
$ pbcopy < /etc/letsencrypt/live/example.com/privkey.pem
$ pbcopy < /etc/letsencrypt/live/example.com/cert.pem
Note: You may need to create a bundle before copying. Instructions can be found here.