In order to help keep responses coherent and to help others find similar questions and answers, please dedicate each thread to a single question when possible.
For the TinyMCE problem, the second column in your database represents the context for the plugin setting: 0 for the Site Context, or another number (e.g. 1) for a specific Journal Context. As you note, in a single journal install, navigating to the “Plugins” tab of “Website Settings” will only affect the journal’s Context ID (in your case, context “1”).
The problem of the links not working after disabling TinyMCE was reported by another user here:
We did not, however, get any more information as to what might have been causing the problem, and I couldn’t replicate the problem. Can you give any details from your PHP error log, or JavaScript console?
The issue with the custom blocks sounds like it might be substantial enough to report as its own post. Can you repost under a new topic where the subject describes what you’ve found?