Flashing icons,? Folder, Circle with bar, Apple on Startup

I have been working on the software of this machine the last 3 hours. It has10.8.5. I've been installing updates stored on an external (all known good). Trashed a lot of duplicates in the download folder. All of a sudden the finder locked up. Upon restart I get very fast flashing of he Apple logo, the circle with the bar, and the question mark folder. I had previously replaced the upper case, upgraded the RAM to 4 GB, installed a larger Apple 320GB (zeroed out) hard drive. Used SuperDuper to transfer the old data. The machine will start from the old hard drive in USB mode. It will not start in safe mode. Using Recovery partition on the old drive, using Disk Utilities says the drive is good. I was able to repair permissions except this "Warning: SUID file"System/Library/CoreServicesRemoteManagement/ARDAgent.app/contents/MacOS/ARDAgent" has been modified and will not be repaired." I don't want to lose the 3+ hours I have spent working on the new drive but I have never seen the three fishing icons at the same time. Any ideas?