Photoshop will actually grey-out the unavailable filters in 16-bit/ch mode. The unsharp mask filter should work. As far as I know, photomerge is exclusively 8-bit/ch anyway.
It shouldn't be necessary, but if you want to completely flatten an image, the command is Layer > Flatten Image. Also, make sure you either have nothing selected, or the entire image selected. If you accidentally marquee a tiny selection, you may not realize that the filter is only working on that one small area.
If you can't figure it out, maybe post a screen shot showing the layer palette.