It's been an awfully long time since I tried running a CLI script...
... From what I remember, the INSTALL command just writes a boot track onto a specified drive (DF0:, HD0: or similar). You can't ever Install CD0:, because that would try to write a boot sector to a CD (read only device, cannot be written on).
If you want to run a CLI or Shell script, you have to EXECUTE it. That could be where the confusion has arisen. You can RUN an executable program, RUN will start up a little separate CLI or Shell for that program. Just typing the program name and hitting the Enter key will start the executable going in the current CLI / Shell.
Hand crafting an Amiga boot partition, I usually;-
1) Format the device.
2) Put a boot track on the device.
3) Copy the Workbench floppy to the device, keeping same directory structure.
4) Copy custom hardware device drivers (anything ending in device) to the DEVS folder, all the Handler files (everything ending -handler) to the L folder. A lot of these were built into 3.1, like CrossDOS for reading PC formatted disks. Had to be put in by hand on earlier revisions of AmigaDOS,
5. Similarly, if you have custom libraries like icon.library, make sure they go in libs (and of course, you need 68040 library or 68060 library if you have such a processor fitted.
Must admit, never tried the above on 3.1. But it should give you a rough idea on what is needed for a successfully booting Amiga and what isn't. S folder (startup-sequence), L folder (handlers), C folder (commands), Devs folder (devices), Libs folder (libraries) and ENV folder for 2.04 and later systems to remember user-preferences. It is often possible just to read a whole CD-ROM (one that boots on a real Amiga) to your hard drive, put a boot track on the drive (Install HD0:) and your Amiga starts up as if booting the drive... Not always what you want, but it is a starting point for a working, booting Amiga.
One complication for you is probably not having a 3.1 ROM chip in your A2000. That's OK with just about every single Accelerator card, you can set the machine to cold boot from it's internal ROM, then read the ROM you want into accelerated FAST memory and reboot to a warm booted, 3.1 OS. You lose 1MB of fast RAM, and having a real ROM chip saves you a reboot, but technically ROM code executed a sideways ROM will run faster than code run from a ROM chip anyway. Your Amiga boots slower but runs faster when it has finished booting.
Come to think of it, RELOKICK software will let you map fast RAM as a ROM on any Amiga, not just accelerated ones. Of course, you need to have plenty of fast RAM fitted to the Amiga in question in order to make that a useful thing.,,
