RAF used a few different techniques for spar cap layups, including the use of their uni cloth in the GU canard. At the time of the video, many techniques were still being perfected. I too was a little confused when I saw Burt and Mike laying up the spar cap with the cross weave.
My understanding is that the spar cap material is designed to be used without the cross weave.
The cross weave does not allow the uni fibers to lay as straight as they can be with the weave in place. If one examines the weave, it is very irregular and obviously only there to keep the roving in place until installation.
The most latest RAF documentation (perhaps there is a CP article as well that I missed) that I can find is the Special performance canard (Roncz canard) instructions, that specifically mentions the removal of the "fine thread that is obviously not fiberglass" and the cross fibers. Perhaps there is a reason that fine thread is red.
The procedure to remove the cross thread is not difficult and I cannot think of any reason to keep the cross fibers in place for spar cap layups.
Spar jig: Good to know if found a new home, it would have been chopped up if you didn't take it. Be sure to measure everything again, I just want to make sure mine is the only plane flying crooked!