Karlovic and Zovko are your best players for doubles, surely? I suppose that neither are great returners, but both have good serves and net games. Dodig would probably be okay, but surely Veic will not be trusted?
Tough tie, but I'd give the edge to Croatia. They have chances in four of the five rubbers (with the exception of Nishikori vs. Dodig) imo, so the question is whether they can win three of them. The obvious target is the Japan #2 in singles - will be tough to beat in both matches, but it can be done. Croatia also has the edge for the doubles imo.
Zovko is a regular doubles player, so he will surely be trusted before Veic. Ivo is also a solid doubles player (defeated the Bryan bros. with his partner Moser) and his serve should help the team largely. Although Dodig played in the doubles final last Sunday in Zagreb, I think Ivo will play, there's probably a reason why he's assigned for doubles, and not Ivan.
The more I think about this, the more I think we will win except if we're 2-0 down after day1.