First, the United States Border Patrol should be re-aligned with ICE/HSI with Border Patrol taking care of Border activity and ICE/HSI focusing on interior. If these two entities were merged you could eliminate a massive amount of redundant middle-management and improve the communications immensely because it would be the same agency.
Second, Customs and TSA should be merged together. Both of their respective jobs are essentially the same, screening people in and out of the United states. This would improve the coommunication between those agencies and again reduce a lot of redundant positions.