Photoshop CS6 Export Multiple Layers with Fixed Top Layer Effect on All

I am trying to Batch Export 200 Images as PNG each with a Top Layer which has Glass Type effect. I actually have 3 different effects and 200 images = 600 unique exports.  
Effect + Layer (1-200)

Using "Files |Scripts | Export Layer to Files"  Turns OFF this Top Layer and only the original images export. This process also takes forever and should be done on subset samples eg 3 images. The PSD should also be saved prior to execution

By making "Comps" it was possible, but still a manual update and individual comp files for each export The need to apply to each comp is cumbersome also, although the exports work "File | Scripts | Layer Comps To Files.."

Should unique each export be managed as layers in groups? eg Effect At Higher level than group or should all related effects and images be located as a group?  The main idea is to change the effect once only to enable changes to all subsequent exports.

Should it be 3 separate PSD projects for each Effect Type?

The Process should be repeatable and minimal effort to update the 600 images. It would be good to know how to STOP the prefix as the files should be named from their layer comp name only

The files should take on their existing name based on their layer name.