Reinstallation of the site must be done with caution; you should do a backup of the database before start.
If you rename your configuration.php file, only install (or copy all files) from Joomla 3.9 and after that rename the old configuration.php everything should work. Once you get access again I fully recommend you to use akeeba (or other backup product) before doing nothing more.
I managed to redo the site (just a redirect problem) but it's good
I reinstalled your extension and then did a scan.
1 / How is it that it find files of the pirate whereas I made a blank installation of joomla 3.9 then reinstallation of the extensions JCE and JCHoptimiser (that I will perhaps be suppriemr)
2 / I have to manually delete these files?
Yes, I know sometimes it can be difficult to differentiate real threats.
Please, take note that the malware scanner IS NOT an antivirus; I designed it to detect patterns commonly used in malware but that can also be used on legitimate files. This could cause more false positives but good news are that detection rates are really high (sometimes no anti-malware engine -more that 40- detect threats that the malware scanner detects).
Taking this into consideration you should pay special attention to those files rated as high, and if you have doubts don't hesitate to ask me.