In case you haven't seen it, check out Oracle's
Packaging Programs in JAR Files tutorial. The links "Working with Manifest Files: The Basics" -> "Adding Classes to the JAR File's Classpath" are also relevant here as they explain how the sshj or other jars can be referenced from your application's jar file.
It might pay to start with a rather limited version of your program and play around with the process of deploying it to another computer as described in Oracle's tutorial. This might save disappointment later, and, if problems occur, you'll have something specific to ask about. It's never easy to come to grips with the nuts and bolts of a new language environment and when you throw 3rd party encryption, logging etc and build tools like gradle into the mix it's very easy to get lost. Good luck!