The way we intended to do this was to send our FF "ground-truth"
collection through Tor, and specifically through the same exit node as
TTB uses. This way we can isolate the variable to the differences in the
browsers, rather than any network or other concerns. In addition, we are
working on developing a method for determining if content is dynamically
generated (and therefore different every time), or broken.
Won't this severely taint your "ground-truth" though? If you're ultimately using the exit-node for both, then you'll really only end up measuring what is friendly to the Tor Browser itself instead of Tor overall. Is that the goal?
If not, with direct access to an exit node, you could run the test direct from that node (not using Tor) for the "ground truth" and then use it as the exit node of choice for the Tor Browser to have a solid comparison between Tor vs Not-Tor.
I look forward to seeing this come together!
-Ryan