Difficulty passing data to PyStan: variable name=N; dims declared=(); dims found=(1)

Yes, it should be list of list, or I usually use numpy arrays.

Is that named list in R?

I Would transform it first to pandas dataframe (if it is 2d) and then use .values

import pandas as pd
...
'X' : pd.DataFrame(my_dict['X']).values

See that the order is right. If you need transpose use .T for the object: .values.T