For the transport module I cannot find a proper statistics of passenger-kms and tonne-kms. Can I calculate this in the other way (e.g. lenght of motorways devided by population, etc) or use another units, for example, percentages for passenger vs fright transport?

Passenger-km and tonne-km is just one method for estimating energy demand for the transport sector. Feel free to use another method of your choice based on the data you have available. You can change the units used in the Activity Level and Final Energy Intensity variables, and even add your own custom units through the Units manager available through the General: Units menu item.

Thanks,

Emily