Overall plan sounds fine, but as you hinted at, I don't think you will find 3 bases that work for all of this. You can find reasonable bases for some of this, but you will either need more than 3 of them, or you will need to do some of these places on their own (not from a base) - probably a combination of both.
In particular, I think you will find that islands do not work well as day trips. You end up with just a few hours on the island (with all the other day-trippers, which means you see the islands at their worst), and spend too much of your day ferrying around.
You should be aware that ferry schedules are highly impacted by high-season/low-season variability - and your travel time definitely puts you out outside of their definition of "high season" (generally early June through end of August). That'll help with crowds, but it will greatly impact your ability to efficiently connect via some ferry routes (in low season, some routes go less frequently, some routes simply don't go at all).
Ljubljana is the obvious base for Slovenia, although if your focus is Julian Alps you might pick Bled or another location outside Ljubljana. Lake Bled is lovely (we did an overnight there), but I don't think we would have been happy staying there (in the town) for days. We liked Ljubljana a lot, though.
For Istria, Rovinj is the obvious pick, or maybe one of the hill towns (eg Motovun). Those Istrian hill towns are small though (less going on there than Italian hill towns, for example) so if you want quiet, they might be perfect, but if you want to stroll the streets at night taking in the scene, you might feel like they're a bit small and limited for your tastes.
Once you get down into Croatia though, it becomes more challenging to find a good base. You might want to fine-tune your list for non-Istria Croatia and take a hard look at a map and travel times...I think you may find that there's no single "base" that works efficiently for "everything else"...from Zagreb to Dubrovnik, that's a lot of territory and getting between your destinations won't be super-efficient.