To boot 10.3 Panther, you need to run XPostFacto
http://eshop.macsales.com/OSXCenter/XPostFacto/
10.2 Jaguar was the last Apple-supported OS X version on the G3. Which version did you have running on your existing OS X partition?
Removing and reinstalling the RAM and VRAM shouldn't cause any problems. If you are changing hardware or adding new components, you may need to reset the CUDA switch, near the back left beside the PCI slots just to get it to startup. If you are just having boot problems, think about getting a new PRAM battery.
With boot problems like this, the data on your disc is probably still fine, if anything it may just need some minor repairs with Disc Utility, but a total reformat probably is not necessary. It's good that you can boot into another partition into OS 9. You should be able to boot from the Panther install discs, it may take a very long time to load everything from the OS X CD, much longer than from an OS 9 disc.
I think you could run Disc Utility from either the OS 9 partition or the OS X install disc. Maybe an expert could give a recommendation if either one is better.