I understand your trouble Sorry to hear about that. I know it's sometimes too much trouble with visas. If you take ferry then you won't have any problems but you will lose half a day for that journey. It can still be fun though.
If you are from South Africa you will need visa to cross through Bosnia. On the Bosnian website "Ministry of Foreign Affairs" they say:
"Citizens of the Republic of South Africa are required visas when entering, exiting or travel…
For everybody that needs more information about visas to Croatia check out this page - Ministry of Foreign Affairs and European Integration
Click on "Regulation on the visa regime (NN 41/08)" on the bottom and …