You seem to have most things covered although now you mention those peripherals 
I'd say one of them is causing the problem for sure.
When in doubt as you already know , strip it down to bare essentals and all 
Apple only gear and start from there introducing things back into your system 
one at a time.
I've had to do the same thing on numerous occasions and you can usually get 
things sorted - it just takes time is all.
I have just done this on a Cube of mine using parts from another as test items 
and eventually I found the problem - a worn IDE cable for the hard drive.
>From the outside the cable looks fine - no breaks, tears or wear of any kind 
>but after testing the hard drive , memory and a few other parts and swapping 
>the cable from the donor machine found that the cable had one wire broken 
>inside the plastic sheathing despite me examining it with a magnifying glass.
Tested it with a multimeter that a friend brought around and on one wire we 
found no continuity.
Lots of cursing but I did solve the problem.Cheap to replace too thankfully.

Re the trackball - I read a while ago about someone else on a Mac forum who 
lost the ball out of the same Kensington trackball and they replaced with a 
white pool ball - it must be the same dimensions. Ha - ingenious.

Stewie



> Date: Sun, 25 Oct 2009 18:28:01 -0700
> Subject: Re: Sleep issue on G4 DA
> From: michaelgm717...@gmail.com
> To: g3-5-list@googlegroups.com
> 
> 
> Hi,
> In the Energy Saver I only have 'Put the Hard Disk(s) to sleep when
> possible. Both the Computer sleep and Display sleep I have set to
> never, and the Display sleep box is not checked, of course. Nothing
> until now has been checked in the Schedule and options menus. I just
> checked 'Allow power button to sleep computer'.
> But, besides all this Mac OS X refs, Mac OS 9 on another partition has
> this issue also when booted.
> 
> I don't know if this Logitech mouse is the issue, that is since I
> didn't install the software and it's not officially Mac OS 9
> recommended, also I have the Kensington Keyboard in a box model #64350
> - It has a power button like the older iMacs. I'd use my Kensington
> trackball, which doesn't really need software for 9 or X, but my kids
> lost the silly ball :P My wife uses the other Kensington trackball
> mouse. I'll do the switcheroo of peripherals soon and report back with
> the results. I pretty much know the ropes of trouble shooting and
> tracking down Mac oddities. - I've had our eMac with the bad caps
> issue that had the logic board and power inverter replaced twice (one
> part each time) and now it's been working mostly flawlessly. The only
> issue with the eMac usb 2.0 is that I installed the eMac tiger install
> for the 2005 eMac and it won't work with fast user switching anymore -
> Still a great deal at only 70 bucks about a year ago now from fastmac,
> thus my wife is the main user of it and I am still Admin of it and I
> use it for more up-to-date things when needed and updating   Mozilla
> apps when needed, etc.
> 
> Anyway, back to the topic. I also have been trying to set up the AGP
> ATi prefs in the ATi prefs pane. I'm pretty sure everything is totally
> set up kosher for my needs and I don't use a TV, so I don't have any
> of those prefs enabled.
> Like I said tho, almost all fans that I know of have the 4 pin molex
> connection option.
> The fan I have is the Kaze-JYUNI Slip stream 120 mm, Model # SY1225SL
> 12SH, 3 pin connector with 4 pin connector included (which I used)
> 12V, 0.53A. I got it from newegg.
> The original fan is a Sensflow Model #  WFC1212B, 12V, 0.44A. So, I
> don't think 0.09A is a big System drain since you can hook up a
> zillion other things like USB powered drives and PCI slot fans, etc.
> This is a lot  of info.  I hope it makes enough sense.
> BTW, thank you for your help so far!!! :)
> Mike
> 
> 
> On Oct 25, 8:15 pm, Stewie de Young <stewies...@hotmail.com> wrote:
> > DOH - what am I talking about- Command - option P-R - in too much of a 
> > hurry !
> > The only sleep problems for any of my Macs was the USB2.0 card as I already 
> > stated and the only time I replaced a main fan was in my Sawtooth and that 
> > was from another so it went straight in.
> > If you still have the original fan you could cut the connector off and 
> > transplant it onto the new one.
> > That would probably stop the fan problem but I am unsure of the display not 
> > waking from sleep.
> > Do you have some display option turned off in the preferences for either 
> > display or energy saver ?
> >
> > Stewie
> >
> >
> >
> > > Date: Sun, 25 Oct 2009 16:26:59 -0700
> > > Subject: Re: Sleep issue on G4 DA
> > > From: michaelgm717...@gmail.com
> > > To: g3-5-list@googlegroups.com
> >
> > > On Oct 25, 6:35 pm, Stewie de Young <stewies...@hotmail.com> wrote:
> > > > Just out of curiosity, why have you connected the upgraded fan to a 
> > > > molex HD power connection and not the two pin like the original ?
> > > > The fan itself won't cause the sleep problem but how you have it 
> > > > connected just maybe.
> > > > I'm unsure what the voltage is for this - 5V as opposed to 7V ?
> >
> > > > Stewie
> >
> > > > From: stewies...@hotmail.com
> > > > To: g3-5-list@googlegroups.com
> > > > Subject: RE: Sleep issue on G4 DA
> > > > Date: Mon, 26 Oct 2009 09:21:25 +1100
> >
> > > > Sometimes third party hardware can cause sleep issues ( USB2.0 PCI 
> > > > cards being the main culprit with this problem ) so it may be your PL 
> > > > CPU upgrade - maybe not.
> > > > I don't think a start button circuit board or fan upgrade would cause 
> > > > this although stranger things have been known to happen
> > > > I'd try a PRAM reset first - press the restart button while holding 
> > > > down the P, R, A and M keys on the keyboard and wait until it chimes 
> > > > three times before letting these go and letting the DA continue on its 
> > > > start up procedure.
> >
> > > > Stewie
> > > Hi Stewie,
> > > I had to connect the fan that way because there was no two pin
> > > connector like the apple original. I've had to do this on my G3 also
> > > with no issues.
> > > I've also reset the PRAM. It's command+option+P+R. I've added a FW 400
> > > PCI and it had this problem before I added this upgrade. I've also
> > > replaced the logic board and still have this issue.
> > > I sure hope it's not the CPU upgrade, I don't think I can send it back
> > > now, it's beyond the 30 day warranty. I usually don't set my Mac to
> > > sleep as I almost always have iTunes radio streaming in.
> >
> > > I'll take a look inside and let you know more about the setup. I'm a
> > > little po'd, this is a nice Mac
> > > otherwise. lol!
> >
> > > -Mike
> >
> > _________________________________________________________________
> > Get Hotmail on your iPhone Find out how 
> > herehttp://windowslive.ninemsn.com.au/article.aspx?id=845706
> > 
                                          
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