You can achieve that by putting code into /etc/nginx.custom.d/codes.conf

make install is already a terrible idea, but if you're ok with that you could just as well install stock nginx, and overwrite /usr/bin/nginx with a symlink to your custom build (which is in /usr/local I guess)

That's because ajenti-v-nginx package depends on nginx package. If you have built your own NGINX RPM, that means that it's not called nginx (instead e.g. nginx1.1.0something). You can either rename the package, or just add provides: nginx to the spec file: http://www.rpm.org/max-rpm/s1-rpm-depend-manual-dependencies.html

By default, non-root users will have access only to websites they have created.

Ajenti V can use any custom-built nginx as long as it follows default initscript naming and default nginx.conf path for your OS.

PHP content type becomes available if standard php-fpm *and* ajenti-v-php-fcgi are installed.

It won't be possible to use different FPM installations with Ajenti V. I recommend instead to set up FPM manually, and then use generic FastCGI content type in Ajenti V instead of PHP.
As for packages, just make sure that your packages provide name "php-fpm" and yum won't complain anymore

Fix uploaded

If your PHP app responds with any HTTP error, nginx will deliver it to client. The thing is that by default, NGINX doesn't forbid any HTTP verbs.

I've also downloaded Thunderbird 31 and both IMAPS and SMTP+STARTTLS seem to work well