Is there a way to specify the order in which to use the photos using Photomerge in LR?
My experience---others may be different:
The way to specify the order is to drag the frames into the order you want while in the Grid view in Library.
I have found that the order sometimes (always?) matters if the 'Perspective' projection option is being used.
The frame order doesn't seem to matter when using Cylindrical and Spherical projection.
Note: Dragging frames will change the 'Sort By' designation from 'Capture Time' or 'Added Order' to 'Custom', but once the pano is created by LR, you can return the Grid view order to whatever is your normal Sort By setting.