Hi,
just install the Enterprise over the Community (upgrade method is supported). About the other questions:

1— Do I have to move the site on the root (out of “site” folder?

Yes, to have new clear URLs without the /site part. This is also needed by the rule, because the destination (after redirection) must exists. And this could happens only after the move...

2— Do I have to take out the base (folder) in my 301 htaccess (move to root or not) ?
- by the way are Redj bypassing or nullify my htacces because I have lot of security & optimisation features in there?

The .htaccess fie is ALWAYS the entry point cause it is parsed by Apache (before Joomla and ReDJ), so ReDJ can't nullify nothing. But I guess you can drop any kind of redirects you have in your .htaccess. Then you can manage with ReDJ.

3— Do I have to take out the base (folder) in your plugin?

Yes, otherwhise any rule like mine (starting with a caret ^) will not work. Leave the field empty, you can do this now.

- and what about the early redirect?

This is needed when you get trouble with rules (e.g. sometimes with Joomlafish). Leave disabled for now. In case of problem I will tell you what to do.

4— Do I have to turn off the Global Joomla config for the .html suffix?

Yes, cause you need to generate URLs without the .html at the end.

Kind regards,
Luigi