Hi, Kevin -
we are really confused why using the pacifist software to open the 'classic' package in the OSX install discs didn't create a new, 'clean' version of OS9 but alas, it did not.
It may have, but it is probable that your machine can't use that OS 9 install.
If your G4 is an AGP model, it did not ship with OSX. Any OSX install disks that include OS 9 are model-specific ones, ones that shipped with a much newer Mac model; because of differences in hardware, it is rare for such model-specific disks to be able to install a bootable OS on another model.
Your G4 AGP can use almost any version of OS 9: early models shipped with OS 8.6; later ones in the AGP series shipped with OS 9.0. You should install OS 9.0 using a CD that originally shipped with an AGP model, or using any retail OS 9 CD of version 9.0.4 or later (the retail CDs have a white label with a large gold 9 on them). Do not use a model-specific OS 9 Install CD from any other model G4 - odds are it will not work.
Once that has been done, you can use the OS 9.1, 9.2.1, and 9.2.2 download updates as needed to bring it up to the version that you need.
Article #75103 - Mac OS 9.1 - Download and Info
Article #120030 - Mac OS 9.2.1 - Download and Info
Article #75186 - Mac OS 9.2.2 - Download and Info
Assuming you want to be able to use OS 9 as Classic as well as a bootable OS, it must be version 9.1 or later. OS 9.2.1 or OS 9.2.2 are more compatible with OSX. If you do not have any appropriate OS 9 Install CD for that machine, I would suggest obtaining a retail OS 9.2.1 Install CD - not only does that have current versions of Disk First Aid and Drive Setup, but using it would also reduce the number of download updates needed.
You can often get retail OS 9 Install CD's at sites like these -
http://macsolutions.com/
http://www.allmac.com/
http://store.yahoo.com/hardcoremac/index.html - Apple Reseller
http://www.applerescue.com/
EBay is another possibility.
Regardless of the source, be sure to get a retail OS 9 Install CD - those are white, with a large gold 9 on them; the retail OS 9 Install CD's have a universal installer; model-specific Install CD's do not.
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Note - you may run into a problem using an OS 9 Install CD if you have wiped the hard drive using Disk Utility while booted to an OSX Install CD. If the option to install OS 9 drivers was not selected at that time, then the drive can not be mounted ('seen') when the machine is booted to OS 9.
Article #106849 - Disk Is Available in Mac OS X But Not in Mac OS 9
Good luck -