I need to have permissions to create and edit workflows custom items but do not need full access to all areas and projects in our JIRA/Confluence environment. I need full rights only for specific Projects, Service Desks and Knowledge Bases, etc.
The permissions are not that granular. You have "full root access", "application admin" and then you're down to project/space administration.
It sounds like you probably need project/space admin on the pieces you are interested in, but you're not going to get workflow access - you need to be an application or root admin for that.
You'll need to talk to your administrators to work out how you can do this sort of thing - develop workflows on dev systems and ask them to promote them, become an application admin yourself, etc.
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