Are you required to comply with the Fly America Act because your travel is being reimbursed by a U.S. Government agency? If so, is it a military agency (that is, the Department of Defense), or a non-military agency (like the Department of Agriculture, Energy, etc)? It appears that if you are being reimbursed by a non-military agency, you are free to fly a Japanese or EU carrier under its own code to or from the U.S., because of "Open Skies" agreements. See the link in Post #5 for more information.