After plenty of trial and error, I have Looter now currently working with Archaeology, right now it is just fragments, not keystones, but since the majority of Archaeology loot is the former then the latter, I think it'll be alright for now to delay the keystones for the next release.
Also as I have not gotten archaeology that high on any character, its been tested only with nightelf, dwarf, and fossil fragments, but the method should work regardless for the rest, but if it doesn't then please post a comment or bug report.
That said, the next version of Looter which will be released in a couple hours once I get the menu option added in (slash toggle already is) with archaeology looting.
Edit/Update: Released. Next in line is support for forms with the smart mounting option.