The short answer is that you cannot do this with a simple "migration"
Jira Server/DC and Jira Cloud are fundamentally different pieces of software. They're from the same people, they have code in common, they do the same thing (issue tracking), and in similar ways. But they're totally different under the hood.
Apps have to be built in totally different frameworks and have totally different levels of access to the applications. A good case is Adaptavist's Scriptrunner. We didn't adjust the Server version to make it compatible with Cloud, we wrote the Cloud version from scratch.
If you look at SR scripts in Server and Cloud, you'll notice that they use different languages. Cloud doesn't support things running Groovy in an app as Server does.
What you will need to do is look at every script and work out how to translate it up to Cloud. Some scripts can simply be rewritten in the right language, but others will have to be replaced with new ways to do it - a totally new Cloud script or using Automations to do part or all of what your Server script did.
And now the shameless plug - a lot of partners would be happy to help you with your migration of scripts up to Cloud. Adaptavist is one of them, but also has a team dedicated to scripting in Cloud, including converting Server scripts to Cloud.
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