There are quite a few variables here to offer a simple answer. Let's work out the easy ones first.
I use this story to help explain the first holdback. So you are walking down the street and your shoes heel comes off you see a shoe cobbler store and walk in you explain your plight you raise your leg up so the cobbler can access the shoe of course he can fix your show while you have it on your foot! Nope! You need to take it off! This is the same issue here the OS is running on the drive as such its like you passing your leg to the cobbler you can't copy active files so that won't work.
The next one is Apple used different OS builds within OS-9 and early OS-X so you just can't use a direct copy method of your working systems drive. So you would need to get the OS installer to install a fresh copy of the OS, you could then copy over any apps you have to the other system.
So if you still have the Grey OS installer disks you should be able to boot up under the installer disk to install the OS. If you don't have the grey disks you can still find them on the online market place's. Make sure you get the official Apple logo'd disks some people will try to see you duplicates which could be junk!
Mac OS-9.2 or OS-X Tiger 10.4.11 being the highest versions these system support.
This is one of the few places you can get the image files Mac OS X v10.4.2 Tiger. Install Discs 1-4 (CD) using your working system to create the CD's. I would still look for the disks if you can.