Kickstart 3.1 is the last official version and it is available on chip either legally from various vendors, or you can get a buddy to make you some if you don't care about staying legal.
Custom "3.9" ROMs have been burned incorporating Boing Bag fixes, these are not required to run 3.9 and are merely a nice touch. If you're skilled enough to make a set or know someone who'll make you one, you're lucky, if not, live with the additional "kick" when you boot up. It's not that bad, really.
Any other customizations to Kickstart really only make sense to hackers messing around with their own systems.