Undersized parties.

I was really looking forward to farming the last of my cards using this process.

The cards seem to drop from the final boss and no items drop does this mean I will not be able to get my cards?

If this is the case could that card be put into the final chest of the dungeons?

You can still get cards. I was going through dungeons on my PLD for books and still getting the card drops from the final boss ^_^