This issue was caused because of an update from 0.8. I had to update the database for pufferpanel so that the web interface reflected the correct SFTP port. The port Should have been 5657. Credit to Lord_Ralex for clarifying this issue.
For each site, you have to create a new nginx/apache config to recognize that the site exists. You must also use subdomains for each of those other sites, as pufferpanel does not permit sub folder installation nor will recognize if you add new folders to it.
So, Solved not solved? I've narrowed the issue down to a migration issue. When new servers are created, it works, but the old servers from before the upgrade from 1.0.3/0.8 aren't working. Just gonna recreate them.
@wafflesofnerds If you're using the default configuration, check /var/lib/servers and look for the JSON for your server. You'll be able to add start-up arguments there. After making the changes, restart pufferd to have those changes take effect.