Final note on this issue: Alexy helped solve the configuration issues, and also discovered that a firewall was blocking port 5443. Even though in the WHM firewall settings, it shows port 5443 is not blocked, Namecheap actually did have 5443 blocked. I contacted them and they unblocked it on their side, and Messenger started working as expected. Below are the 2 correct configuration files for anyone else that has issues getting Messenger to work. Obviously you'll need to edit the information to reflect your certs and paths and so forth.

config.json

{
"port":5443,
"mode":"development",
"log":"log.log",
"domains":["*"],
"transformer":"sockjs",
"root":"/home/witcamkd/ssl",
"cert":"certs/witches_community_c6bfc_dd0a1_1632095999_2e6102967f7476c1657e786b02273e00.crt",
"key":"keys/c6bfc_dd0a1_60b34c1e7ac8d1d925c6445b38a52c77.key",
"OFFLINE":0,
"ONLINE":1,
"AWAY":2
}

package.json

{
"name": "jot_server",
"version": "1.0.4",
"description": "Jot Messenger",
"main": "app.js",
"dependencies": {
"isip": "*",
"nconf": "0.10.0",
"primus": "7.3.0",
"safe-buffer": "^5.2.1",
"sockjs": "*",
"winston": "^2.4.0"
},
"repository": {
"type": "git",
"url": "git+https://github.com/unaio/jot-client-una.git"
},
"author": "UNA Inc <support@una.io> (https://una.io)",
"license": "MIT",
"bugs": {
"url": "https://github.com/unaio/jot-client-una/issues"
},
"homepage": "https://github.com/unaio/jot-client-una#readme"
}