If the 3000 and cd rom are working well under 3.1 , it should be fine to go to 3.9.
The install of 3.9 asks you to create a Emergency floppy. Then it asks you to boot from the ER disk and then install 3.9 on top of 3.1.
Even if you have the improved "pink" cd version of 3.9, you should be ready to install Boing bag 1 and 2 for 3.9. These improvements fix some of the issues from the "red" cd and "pink" cd 3.9 install.
Then be ready to tweak the system to your resouces and likes. i.e. I removed the dock and setup the "other memory" from prefs/workbench.
