No. It is not necessary to restart JIRA when you change the TemplateMe! configuration.
No. You can only edit the templates that you have created with this add-on.
Yes. All TemplateMe! configuration details, including the actual templates are stored in JIRA's database. You will keep them during JIRA or add-on upgrades.
Yes, TemplateMe! is compatible with JSD Projects notifications. However, all the customer portal notifications won't be overriden.
Yes. Create a new empty template and then go to Tools > Source code in the templates editor:
Then paste in the source code pop up screen your custom made template html and save the template.