Sorry for the very late answer.
We calculated the work function for each of basis set in the Cerda parameters, and set the vacuum level such that it gives the correct work function.
Now I am curious. How did you calculate the work function for all those elements? What reference structures did you use? And what do you mean with "the correct work functions"? (The same as with Hoffmann or Müller basis?)
If you want to combine the new basis set with another basis, you will only get a good calculation of the vacuum level is defined using the same method in both basis set.
I combined the new basis set, which I derived form the Cerde_Graphite one, with other Cerda parameters of various metals. I determined the vacuum level of my new carbon set so that the Fermi level of the new set equals the Fermi level of the initial Cerda carbon set. This appeard reasonable to me. Now, how bad is this approach? And how should it really be done?
By the way: I combared the final results (transmission spectra) with DFT and it looks quite nice...