1. there is no option to shut down AmigaOs, so just switch it off. However you must not switch it off while disk accesses are still on the fly, so check that all lamps are off first.
2. you can't. After you formatted a floppy disk, open a shell window and enter Install DF0: to make it bootable.
3. usually not. Only if the game is stored on an AmigaDOS disk which is readable from Workbench, you might have the chance to insert the call to JoyMouse into the startup-sequence file on the disk. If the game is stored in its own format where the bootblock contains the code to read the data, there is no way to do anything else.
4. there is no Workbench version 2.3. There is 2.0 and 2.1, then follows 3.0 and 3.1. WB 3.1 is the only release still being sold, but it needs Kickstart 3.1 also (which is still being sold either). You might look at Ebay or other second-hand sources for copies of Workbench 2.1.
Bye,
Thomas