I have done this numerous times, always with Hertz cars but I think most others are smilar. ITA-SLO only may need to buy the pass for toll, can be doen at most border crossings. SLO-CRO usually no formalities nat all; CRO-ITA sometimes a glance, but I have had nothing more. There is a facility for customs and sometimes they ask for a show of passports. I have also passed through Bosnia, Hungary, Romania and Montenegro without incident. Most car rental companies do not cover insurance for Romania and Kosovo, but do for the others.

Check on the car rental terms and conditions, usually available on the website to find out if you need supplemental insurance or have prohibitions in one country or another.

If you're using a portable GPS AdriaMaps has a pretty decent one for Garmin that covers the former Yugslavia, and has most locations in Slovenia and Croatia, but not all points of interest.