Hi Chitrak,
The extended molecule functionality works for any nuclei. You probably get the "unknown nucleus" error because you replaced H1 with some other nucleus at the "nuclei" line, but left it at the "options" line (in the -sysch$N option). This combination is indeed meaningless.
Regarding the other question, you are on the right track. For an example of how you can set up fragments of large complex molecules (including the CSA tensors) for simlutations in SpinEvolution, check out the pdsd example. Or just read the sections of the Manual concerning the Extended molecule, Local coordinate systems, and sys2ext_map variable. Depending on how you will be setting up your extended molecule, you may also find useful explanations in the Construction of the molecule section.
Best regards,
Mikhail