NAMECHEAP Work Around
So I managed to get a LetsEncrypt certificate to work at NameCheap. It does require access to a shell account that you can work in separate from the NameCheap hosting.
1) Log into your Cpanel and go to SSL/TLS
2) Create a CSR from Cpanel
3) Go to https://gethttpsforfree.com and enter the CSR
4) This is where you need access to a shell account that can work with OpenSSL. Even running in a VM on your own computer will work. Follow the instructions to create an Account.Key/Public Key and Signed API requests.
5) Use File Based/HTML Verification to verify your domains.
6) Create the files on your computer as text Files. I used Bitvise to connect to SFTP on the server because it lets me see hidden directories. Create the hidden directory as instructed, upload the files and remove any extensions (.txt)
7) Verify your domains, if you did everything correctly, it will read the html files and issue your certificate. If not, you have to start over.
8) Go to CPanel back to SSL/TLS and install the certificate to the server.
9) Install SSL to your website.
Congratulations, you have LetsEncrypt SSL on the NameCheap hosting server. Only reason why I figured this out instead of moving the site is because I just paid for a year of service and moved all my domains to them before I found LetsEncrypt. So Id like to run those out if I can before moving again.