Yes, the flash stick autostarted so install started over which is why its best to use the one-time BIOS Boot menu key with the HDD set first to boot.
You can just pull out the flash stick and force another reboot to have it continue install. Or do it over but pull out the stick when it has its first restart.
And yes, I would move the PC HDD back to first boot device after install.
Follow the same steps as in
http://www.sevenforums.com/tutorials/219487-clean-reinstall-factory-oem-windows-7-a.html#post1839164 to handle drivers and set it up perfectly. Get online then run all rounds of IMportant and Optional Windows Updates, after enabling
http://www.sevenforums.com/tutorials/2803-device-installation-settings.html. After requested reboots go right back to Check for Updates. After they're all done import any drivers still missing in Device Manager.