Hi Steve,
Sorry about the delay in getting back to you. I have been travelling overseas during the past few weeks.
I think you are right as we removed this from the CSS & JavaScript Toolbox submenu and placed it in the Plugins section. Come to think about it, maybe we should also have it in the submenu. 🙂
Now you should have the latest version of the CJT Free plugin from WordPress.org installed (at the time of writing is version 8.2).
Then when you install the latest version of CJT Plus, which I believe is version 1.1.1, you should be able to click into Plugins and see the new Setup link under CSS & JavaScript Toolbox PLUS. You should see this as: Deactivate | Edit | Setup.
Hope this helps.
Regards,
Damian Baker