Read through all the posts and checked everything but can't get multiple sites

I checked all the posts and everything is fine, rebooted the server / restarted services check the vhosts, looked at the log files but I still can't get domains to point to the directories that have all the files, checked and renamed the index.html so index.php is read.

Could this be an .htaccess issue somewhere?

Also tried the cpanel import all I got was the structure and html data no mysql or emails. 

Also when I boot now I need to have my usb installed and boot from there.  How can I force a boot from the boot partition on the local drive?