Probably an internal HD failure

Computer froze  and unable to do anything other than force restart.  Got the flashing folder with Question mark.  Disc utility on system cd unable to locate internal HD.  I then hooked up two external HDs and was able to install new 10.6 on  one of the newly formatted  externals.  The other external HD contained my time machine backup.  I was able to boot computer using the newly installed system.  The finder was able to locate the internal HD but the name was changed to "Media" from Macintosh HD.  Get info said it had 0 bytes and little else.  I then restored the time machine backup to the external HD containing the new system.  NOW,  the internal HD is on the desktop with many if not all the files.  I was able to repair permissions and verify it needs repair but unable to repair because it cannot be unmounted even though no files open. Tech Tools on apple care cd wants to fix it but predicted repair will loose alot of data.  As far as I can tell the timemachine backup is good on the external with no apparent data loss.  Can I trust the internal HD?.   Should I do the Tech Tool Repair  Any problem going with just using the external USB drive?.   The performance is ok for what I use it for.  At the very least should I reformat the internal HD so I don't have duplicate but likely corrupted data?Replacing the internal HD seems a little beyong my skill leval.   Thanks

The first thing you should do is make sure your important files are backed up. I personally wouldn't proceed until that has been done.
You indicated that there are file permissions issues. Have you verified the hard drive itself? You can use the Disk Utility verify disk option, but I also suggest checking the SMART (Self-Monitoring, Analysis, and Reporting Technology) logging feature built into your internal hard drive to see if the hard drive has reported any issues. You can use the Smart Utility in the demo mode to check the status.
http://www.volitans-software.com/smart_utility.php

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