Probably the first thing to do is to eliminate the entry ways the birds have to get inside your museums. One way is to cover all openings with glass, or at least with screening. They are a menace to your staff, your visitors, and to your collections...the National Museum in Karachi, Pakistan had the same problem because parts of the museum were open to the outdoors. They can enter through large cracks as well. You also may want to consult with some qualified conservators in Portugal, or contact the conservation committee of ICOM. Good luck!