1st Gen MacPro Wake Up, HD activity takes up all CPU cycle w spinning ball

Since I have added an external HD (750GB) to my n-basestation as an NAS, every time I wake up my Mac Pro, the HD will be busy doing something (I have no idea what it's doing as I can get the activity monitor to come up until the HD stop doing whatever it's doing) for somewhere between 5 minutes to 15 minutes before the CPU is freed up to attend to other stuff like reconnecting the Mac to the basestation, connect iChat to the AIM server, etc.
This never happens prior to attaching the HD. It's extremely annoying. Anyone have any idea as to how to get the computer to wake up right away?
Thanks,
Sherman

A lot of what you describe sounds like a failing HDD. The one failing of OS X, is that Disk Utility and AHT tend to rely on the drive's internal SMART diagnostics, which isn't always accurate. Sometimes you need to actually stress the drive a bit to find the problem.
And I've seen many iMacs with failing HDDs that then start heating up abnormally, which then causes the fans to kick in (if you're lucky, some have had their logic boards cooked) to try and blow out the excess heat.
Now you seem to be confused as to what system you have. In the subject you say it's an iMac G4, but your signature line says it's a G5, which I'm more inclined to believe since you say it has iSight. Unfortunately for you, that is the model where Apple changed the way the iMac is taken apart. Used to be pretty simple. Loosen a few screws and pull the back cover off. Starting with your model, you have to remove the display to get at the HDD.
Still, all things considered, having the HDD replaced is pretty cheap compared to some of the other things it could be. Since this is a G5 era system, there's always the possibility that the logic board has some bad capacitors, which would mean the system's done for.
I'd really recommend you take it to an Apple Store or local AASP shop where they can run some more detailed diagnostics on it. I'm betting they'll either find a bad HDD or bad caps on the logic board. The former shouldn't be outrageously expensive, the latter means start planning the funeral.

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