Thanks for the tips.
I wish to reduce the amount of extra variables in this. My current understanding tells me that if I connect another computer to the QFX, that the extra data would be generated through that computer and its own interface, which might add to the bottleneck.
I wish to test from QFX A, over 100G line, into QFX B and see if there is a bottleneck at all. It sounds like the only real solution is the one that you made: add those hardware deices directly to the QFX on both sites and let them send data to each other. This seems to be a costly option that I would have to investigate.
I would have thought that Junos by now have some commands that will simply push as much packets as it can over an interface and take some statistics from that. It seems that Juniper does not natively support such rudementary tests.