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if the PRAM battery was maintaining System preferences in memory could this have been lost and causing the problem with booting up?
No, at least not that I know of. It mainly keeps things like the time/date, how fast you want the mouse to move, how fast a double-click is, mostly stuff that you can set up easily when it gets a new battery.
Since the hard drives are usually pretty well enclosed, I'm not sure why they don't boot up. The PRAM may keep that kind of info, but the OS usually just keeps looking for a bootable system on whatever is in the box. But it might be a good idea to check the connections. And also reseat the RAM.
The CD reader does have exposure to the environment, however. There could even be real bugs in there!
Other than that, it may just not be able to un-park the reading head due to smoke tar condensing on the mechanism. Or even pet hair could be in there. Some of the dust could probably be removed with a can of compressed air.
As a last resort, you might be able to connect this Mac to another one via FireWire. You may be able to start it up in Target mode. It may then be able to be seen by the other Mac and you can get all the data off those drives.
Please let us know how things go!