Hi Tobias,
I hope you are able to get things working with VOTCA, but in case you are unable to, I am going to be adding the feature you describe to the KMC software package that I am working on called Excimontec. You can find it here:
Currently, only cubic lattice KMC is implemented, but the next dev phase will be focused on allowing users to import data (from VOTCA or other) to form an undirected graph for charge transport simulations, among other more complicated device relevant simulations. Sign up for the Excimontec mailing list if you'd like to stay up to date with the development of these features over the next few months. Perhaps your problem case would be a nice early test case for the new code. Contact me with more details if you are interested.
Best,
Mike