So sorry for the late answer, I don t know if what am saying gonna help !! well...
U should at first keep in mind that CNN are after all used for Images classification not matrix , rather than using CNN u can use proudly the RNN or LSTM. other wise if somehow u r obliged to use CNN, u ve to start from the concept above and think about making ur data look like images, how ... simply u can represent the data using plot then spectrum then fit the given images into ur CNN.
Best of luck !