Well I did get it start up off the CD like I said last night and ran the
disk utility and got to start normally then ran Macjanitor and
Permissions repair and restarted, I thought things were cool. Well
this morning all was froze and now I get a flashing folder, I guess it's
trying to boot off OS9 because it can't find OSX then it goes to the
circle with the slash. When I try to start up off the CD the installer
comes up and when I try to run the disk utility, instead of the installer, it
can only find 1 of 3 hard drives, the 20G that is installed below the
Superdrive and contected on the other bus do hecky. It can't see the
40 or the 80 on the ATA bus. I'm baffled about this one. The 80G is
my main drive and the others are set to slave. The 80G is only about
2 months old and to be quite honest things just never seemed quite
right since putting it in, kind of sluggish and flaky. It's a Seagate 80G
with 8mb cache. Where do I go from here? It looks like it's going
to be a long weekend.
Thanks Grateful11

Can you choose the startup disk while booted from the CD?

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3GHz - The clock is STILL ticking Steve.

No, the only choices it's giving me is "Network Startup" and the 10.3.2 Installer Disc 1.

It means that it can't find a valid BootX file on your drive, which can mean that a hardware failure is causing your Mac to fall outside of spec for the OS that you have on the drive or it could mean that your drive is dying or it could mean any number of other things.

Zap PRAM 3 times, find your hardware test CD, boot from it and run the extended tests.

What MacMagus said, plus if you don't already have it, get a copy of DiskWarrior, boot from that, and see if it will recover your drives and data...

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)

It's telling me that this "Apple Hardware Test does not support this
machine". I bought the tower used a year and half ago and the disk
came with it and it said on the disk it was for a G4. It's possible it
could have came with the Cube I'm on now. I believe it's the only
Hardware Test disk I have.

That's a bit of a problem.

This is not unlike shooting in the dark now.

You could try putting in a new PRAM battery. It might be that simple. You can get a new battery at Radio Shack for something like $15 dollars or at Microcenter.

You could also try simplifying things: unplug all drives other than the boot drive, make sure that the boot drive is set to Master and that the cable is plugged into it tightly and that it's plugged in at the end of the IDE cable and not the middle.

Then boot with the installer disk and see if it finds the drive and can repair it.

...and there's the tried-and-true "pull some RAM" and see if the symptoms go away.

Just now when I restarted , which was one option the Test Disk gave,
it started into OS9. It is installed on the 40G which I believe is
second from the end of the IDE cable.
Grateful11