@vinsite54: Sorry for not updating this topic. I have solved it after 2 weeks of struggle. I have a dedicated server (Ubuntu). I used ClamAv: https://help.ubuntu.com/community/ClamAV
to scan all my websites in my server, and I found hidden malwares in all my wordpress websites theme directory mainly, and more malwares hidden in other locations. Do not panic! Just run a scan with clamav and it will generate a report of all the locations of the malwares, then you just have to delete them manually. Then go ahead and do a fresh install of your wordpress website(s). The best way to do it is to delete all wordpress core files except – {/wp-content/ & wp-config.php} reupload fresh files from the latest version. Then go to the admin panel and re-update again. At this point you should be able to edit your htaccess back to it’s old settings, but first change htaccess chmod 444 to 644.
You might also run into another issue maybe now maybe later, but it’s easy to fix it, check my answer to this post: https://stackoverflow.com/questions/29896125/wordpress-database-returns-error-500
you can keep this post updated and i will read you up.
Best of luck bro,