Select by Location/Export Multiple SDE Feature Classes into GDB using ModelBuilder

I am trying to recreate a somewhat tedious workflow using ModelBuilder. The (manual) workflow follows these simple steps:

1 - Select by location: 39 input features residing in an SDE database; select features that intersect AOI(s) polygon layer. (These are not ALL of the layers in the SDE database.) We commonly manage these by using them from a .lyr file.
2 - Extract Data (Distributed Geodatabase) into new file geodatabase.
3 - This geodatabase is used as the reader in an FME Interoperability tool.

I have tried my hardest and searched high and low for a way to automate the extraction process, to no avail. Here are the issues I've found:

1 - Create Replica does not work because the SDE database is not versioned, nor is it preferable since there's no reason for the output database to be transactional. However it does allow for a replica area (AOI).
2 - Package layer does not work because the envelope is defined by the extent of the AOI, which may be multiple polygons over a large area and cause too much data to be extracted.
3 - FME only tools are, from what I can tell, too slow. PointOnPolygon has to read the entire input before operating, and it's just too much data.

I'm trying to avoid having to make 39 copies of Make Feature Layer > Select by Location > Feature Class to Feature Class. There has to be a better way! A tool that would consume each feature class directly or from a .lyr would be preferable, then export the selected/intersecting features to a .gdb. It doesn't really matter how it works.

Thanks for the help!