With the two uncompiled mxml files, have you added those widgets to your src/widgets folder? Once that is done, click on project and then properties in Flash Builder, click add and then browse to the src/widgets and then your widget folder. Search there for the mxml file that you want to add. Once you select your file, then make sure you click the radio button that says Do not optimize that way you can load the compiled .swf and associate .mxl file into several applications.
Second once you complete the above click project and clean. This will clean everything in the bin-debug folder with a new compiled widget with new .swf, and .xml folder.
Hope that helps.....