Difference between pem, crt, key files

Those file names represent different parts of the key generation and verification process. Please note that the names are just convention, you could just as easily call the files pepperoni.pizza and the content will be the same, so do be conscious of how you use the filenames.

A brief primer on PKI - Keys come in two halves, a public key and a private key. The public key can be distributed publicly and widely, and you can use it to verify, but not replicate, information generated using the private key. The private key must be kept secret.

.key files are generally the private key, used by the server to encrypt and package data for verification by clients.

.pem files are generally the public key, used by the client to verify and decrypt data sent by servers.

.p12 files have both halves of the key embedded, so that administrators can easily manage halves of keys.

.cert or .crt files are certificate signing requests, used by a trusted third party to verify the ownership of a keypair without having direct access to the private key (this is what allows end users, who have no direct knowledge of your website, confident that the certificate is valid). In the self-signed scenario you will use the certificate signing request with your own private key to verify your private key (thus self-signed). Depending on your spefic application, this might not be needed. (needed for web servers or RPC servers, but not much else).

A JKS keystore is a native file format for Java to store and manage some or all of the components above, and keep a database of related capabilities that are allowed or rejected for each key.

The commands you list look fine to me, and I don't see a question beyond asking what the different files are for. If you need more information, please enrich your question.