Jeremy, check that your Atlassian ID is the email associated with your JIRA Cloud account, and that you're logged in to that account while trying to set this up.
Or, the preferred method is, from within JIRA, select the admin cog, choose Add-ons > Find new add-ons, then search for "Salesforce" and find the appropriate add-on within the Universal Plugin Manager (the the screen within the application you should be in is called the UPM, or Universal Plugin Manager).
Let me know if this helps.
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