>Where do we put custom Jar files when building the Docker image?

/databricks/jars

>How do we update the job configuration so that the job’s cluster will be built with this new Docker image, and how long do we expect this re-configuring process to take?

You could update the jobs with the new docker image by calling the update jobs api and specify

"docker_image": {
    "url": "databricksruntime/standard:latest",
    "basic_auth": {
      "username": "<docker-registry-username>",
      "password": "<docker-registry-password>"
    }
  }

under job settings