Welcome!
AmigaOS version numbers can be a bit confusing if you're new to the platform. From oldest to newest the release order of 3.x for the 500 is 3.1, 3.5, 3.9, 3.1.4, 3.2. (3.0 was only for the 1200 and 4000.)
3.5 and 3.9 ROMs do not exist (those OSes were a software-only upgrade), except for custom versions that users have compiled and burned themselves. Cloanto's 3.X ROM is largely - but not entirely - analogous to what a 3.9 ROM would have been.
To nitpick a bit, the 2.x release for the 500 was 2.04. (The actual 2.0-2.03 were essentially beta releases for early 3000s; 2.04 is the stable version) 2.05 was intended for the 600 and adds drivers for that machine's IDE port and PCMCIA slot. It's otherwise identical to 2.04. It will work perfectly fine in a 500 but there's little point to it unless you've added a 600-style IDE port - the TF536 *might* fall into that category, but if that board more broadly requires Kickstart 3 then this point is redundant.
Anyway, if you've got a 4-slot switcher with 1.3 and DiagROM already set, my recommendation is 3.1 and 3.2 for the remaining slots. 3.1 has decades of history behind it and is extremely well supported and stable. And you can install 3.9 on top of it if you later decide to do so. 3.2 incorporates almost all of the functionality of 3.9, including more modern hard drive support, plus many other subtle improvements, but it's still quite new and little issues/quirks are still being discovered.
There is almost no software that works on 2.04 but not 3.x which is why I left that one out. If you really want to make sure all your bases are covered, then go with 2.04 and 3.2. If you do install a 2.04 ROM make sure to use OS software version 2.1, which is a major improvement in ease-of-use.
3.1.4 is a halfway point between 3.1 and 3.2. Might as well go for either of those instead of 3.1.4.
