What you are asking for may not be possible with the OS9 VNC server. As far as we know, that server can only run as a user process, which apparently gets shut down when you log out.
One possible way around this would be to use an external VNC server. One that we’re aware of is the AdderLink IP KVM Extender from Adder Technology. This is a hardware device that is physically connected to the SUT’s keyboard, video, and mouse (KVM) ports, and has a built-in VNC server that Eggplant can communicate with. We haven’t tried this specifically with a Mac OS 9 machine, but it has proven useful with Eggplant for other cases where a VNC server is unavailable (including testing functionality in the BIOS on a PC at boot time).
Another approach you might consider would be to run your application in the Classic environment under Mac OS X. That way you would be running the OSXvnc server, which is more robust than the OS 9 server and benefits from regular maintenance updates.
This ought to be a solution to your second problem, at least, and allow installing software in the OS 9 environment even if that process requires all other OS 9 software to be shut down, since the VNC server will be running outside of that environment. We recognize that there may be some slight differences between running your software in the Classic environment versus natively in OS 9, but this may be a viable alternative for those tests that can’t be done natively.
I hope these ideas are helpful.