Budapest to Split

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My husband and I are traveling to Budapest, Dubrovnik and Istanbul at the end of this summer.  We are flying into Budapest on August 25.  We are hoping to take the train from Budapest to Split (and then bus or ferry to Dubrovnik).  What is the best train to take to Split?  Should we travel through Zagreb?  Do you recommend an overnight train?

Thank you so much for your help!  This is an amazing site!

This year till August 27 there suppose to be couple direct overnight carriages from Budapest to Split (5pm-7:44am). They get attached to Budapest-Venice train which carries them till Zagreb, there within the half hour those carriages are being reattached to overnight train to Split. 
In case you want to travel during daytime (scenery outside sometimes is rather nice), then you will need to take the morning train Budapest-Zagreb (6:30am-12:59pm). From Zagreb to Split you can depart at 15:19pm (arrive 20:52pm).
 
Due to the special Hungary-Croatia rail tariff discount it is actually cheaper to purchase r/t ticket, then one way. Fare for r/t ticket Budapest-Split suppose to be app. 66 euro.
Hungarian railways may as well come up with some kind of special discount for the route, but no info available yet.

Other option on how to get from Budapest to Dubrovnik area by train is to take Budapest-Pecs-Sarajevo-Mostar-Ploce route (daytime Budapest-Sarajevo and early morning Sarajevo-Ploce). Sarajevo-Ploce route is one of the most scenic routes in Europe. But as you can see such route will require transit via Bosnia and Herzegovina. Sarajevo in this case can be reached by daytime and overnight trains from Zagreb too.

Thank you for your response.  I didn't realize that there is a train from Sarajevo to Ploce.  I bet that is a beautiful trip!  It is going to be a difficult decision on which train to take.  I have another question.  Do you pay a tourist visa fee for each country you go through on the train, or do you pay only if you leave the train?

Do you pay a tourist visa fee for each country you go through on the train, or do you pay only if you leave the train?

In almost every case it will be the first option. If, due to your citizenship, you need a visa to enter a country you will be forced to get at least a transit visa and it doesn't matter whether you leave the train or not. In such cases you undergo full scale border crossing procedure.
Usually visa is not needed only in cases when a train passes small part of the other countries territory and does it without any stops, like Bar-Belgrade trains pass 9km part of BiH or trains from Austria nonstop pass couple km of Liechtenstein's territory on their way to Switzerland.