Hi
running three OS on the machine would be no problem:
Buy a KickflashOS4 from Individual Computers. Using this flashrom in conjunction with a 2.04 Kickstart ROM you could easyly switch between OS 2.04 (disable the KickflashOS4 via a switch), OS 1.3 (by pressing the fire-button of a joystick connected to the second mouse-port) or OS 3.1 resp. OS 3.9 (depends on whether the ROM-update is placed on HD or in the Kickflash ROM or not).
So you have three Kickstarts in ROM (EPROM) and the system boots very fast regardless which OS you are using.
There is a tool called "ColdReboot" available at Aminet. This tool does remove all patches made to the system and everything loaded to memory, i.e. it resets the Amiga into the state it has just after it is switched on. This should work.
ftp://de.aminet.net/pub/aminet/util/boot/ColdReboot.lhaNoster