Congratulations. I've been using Macs literally for decades all the way back to the little Mac Plus and you have managed to come up with a problem I've never heard of!
I too, have a G4 with multiple drives specifically for system/apps and audio/data etc. I cannot imagine how this is happening to you.

Seriously… this would require guessing out of the box. Stuff like:
1) Somehow both drives have the same ID# ?
2) You used a foreign IDE ribbon cable?
3) One or both drives already had System and App files before you installed it/them in the machine and you only just now noticed?

When you "set up" a computer, you normally start with blank drives. AFAIK, there is no way your Mac would write duplicate files in two locations.
So, more info is needed here. What model G4? How did you set it up beyond “sticking in” two drives?

When i do exactly that it shut downs, same thing with of command

Not good.

Too bad you’ve no other MDD mobo to test with the ATX.

And without visual comparison of the two processors — can’t tell if one has been heated more than the other… in which case, one of them has possibly failed or is failing. There’s also the possibility that the daughtercard itself may be warped and not making full, adequate contact(s). [We’ve seen that before.]

*Applying direct, downward pressure on the heatsink (with the palm of your hand) might provide different results?

When you cleaned off the old heatsink paste before repasting, what condition was it in? Totally baked? And you don’t remember if one processor appeared different; as if it had been overheated?

Easier to remove the CPU and visual check. And easier to replace the CPU, rather than to pull and replace the mobo.

So if you go to the… time, trouble and expense of replacing the motherboard and then discover no change, you’d need to then possibly replace the CPU.

In the meantime, you can very closely inspect the mobo (top and bottom) looking for any signs of overheating or other possible damage to the myriad of tiny electronic components and traces.

So, if the ATX PSU is okay and functioning properly, I’d suspect the CPU and / or the motherboard at this point. However, the questionable GPU may be the root of your problem. And maybe after its replacement, conditions might change?

BUT with that processor warning… well, who knows?

Sorry, no quick-fix easy answers for you. Maybe I’m missing something, but as always… not easy to diagnose problems without the advantage of having machines close at hand.

If you’ve already ordered the new GPU, please report back if any change after installation.

Too many variables at this point.

When i do exactly that it shut downs, same thing with of command

Try booting while holding down the "t" key.

As for tdm it doesn't work on this thing yet still maybe because of dvd drive being not present, but i can put my spare hdd into mbp 2008 and boot from it (i reinstalled 10.4 and 10.5 this way on 35 cycle ibook)
Also this is first batch mdd from 2002, that supports native os 9
Expansion slots are not related because i don't have any expansion cards and i removed modem

Well, that GPU may make a big difference.

AND probably, makes no difference... pin 18 or 19?

Can you boot your MDD into Target Disk Mode? If so, then you might be able to run diagnostics on it using the G4 iBook? Maybe.

Currently I am also looking for… ASD v2.1.5 (Apple Service Diagnostics) for the MDD because if you cannot access your machine from the G4 iBook using Target Disk Mode to possibly run diagnostics… then ASD v2.1.5 might be a better, more direct route. (If you don’t have an earlier model of MDD requiring a different version of ASD).

I’ve already forgotten if you’ve a firewire 400 or 800 MDD — or perhaps you’ve not specified the exact MDD that you do have? And then again, in order to use ASD you’ll have to have an onboard DVD drive in order to boot from it. (Or a bootable external DVD drive.)

Another little note: Disconnect and or remove every non-essential peripheral (and network connection) AND internal cards... from your machine, other than the absolute bare essentials for it to function.

AND it’s odd that the machine will only accept 1 stick of RAM? This leads me to also wonder IF maybe the machine’s motherboard was somehow possibly damaged prior to your possession? (Especially if we can possibly rule out ATX PSU problems.)

*The “correct” version of ASD for your specific machine, option-key booted from a burned disc allows one the option of either booting into Open Firmware or via the OS X operating system. BUT you have removed the DVD drive in order to accomodate the ATX PSU.

Will the MDD accept and read & write to a USB connection? (Thumb drive or external USB drive.)

Done, will test this after i will get my new radeon 9000 because original gpu lacks vga and is damaged

Been playing with my G4 today - had a change of heart regarding soundcards - I really like the RME cards (and have never had an issue with one) whereas the Audiophile was buggy and troublesome from the start.

So I removed the M-Audio.

To uninstall properly is it just a case of searching for all related files and deleting? So - Extensions, Settings, Applications... anywhere else?

When I set up my G4 I stuck two (IDE) hard drives in, thinking one for data and audio files and the other for apps and system files.

I've noticed recently that the Audio/Data drive has ended up with duplicates of all the system folders, including applications. They don't seem to be identical to the folders on the system drive, but they do seem to have some identical files...

Apologies for my ignorance but (as someone who is a PC native and a mac dabbler) this seems very odd!

Performance considerations aside it defeats the object of having everything neatly sorted into the two drives. In an ideal world, in the event of issues, it would be nice to be able to nuke the system drive, and reinstall but keep the data...

As things stand I'd be tempted to merge the two drives to keep everything clear and simple - but will that break my system? I've got way more space than I need anyway and at this stage I have firewire and SCSI drives than I can use for audio projects, if needed...

Or am I looking at things the wrong way?

Apologies again if I'm being very stupid. I haven't plugged the machine in for over a year so I'm definitely rusty on what's what!

I have brown and not grey cable connected to pin 19