Yes, the reddish cocoons (pupae) are probably from house flies. You can feed them to fish if you have them, or bury them to prevent the adults from emerging.
Leave the paper dry and the BSF will finely shred it eventually.
The BSF adults that are visiting your bin are females looking to lay eggs. Within 3-4 weeks you should have a healthy colony going.
Between the paper and not adding new food scraps you should see some reduction in the other fly species in a day or two.
