How can I make big confusion matrices easier to read?
You can apply a technique I described in my masters thesis (page 48ff) and called Confusion Matrix Ordering (CMO):

Order the columns/rows in such a way, that most errors are along the diagonal.
Split the confusion matrix into multiple blocks such that the single blocks can easily printed / viewed - and such that you can remove some of the blocks because there are to few data points.

Nice side effect: This method also automatically clusters similar classes together. Figure 5.12 of my masters thesis shows that:

You can apply confusion matrix ordering with clana