Hello,
we just received your .htaccess via email.
You have there a lot of extra directives that may not be allowed and thus be causing this 500 error.
Start with commenting them out and you will see which one is the reason.
E.g. comment out SecFilterEngine off, SecFilterEngine off.
Also wrong value or that usage of php_flag directive may be causing this. Depends if your server configuration allows overriding particular settings.
Anyway, your server administrator should be able to help you with this. We can also do that, but as this is related to your specific server configuration, not connected directly with JoomSEF, so adjustments there would be a paid support option.