Aaah. Ok. When you said 'crate,' I thought you were referring to their cage (some people use large dog crates for cages). But you meant the carrier. Yeah, the carrier is really close quarters, so that carrier has to start moving the moment you get them both in there -- even if it is just walking the carrier around to get it to the car. It is the movement of the carrier that stresses them -- the idea being that they are more worried about what's happening around them than they are about the rabbit beside them.
Unfortunately, they have had the tornado fight which sets a different tone. You did right by keeping them separate for the following 9 nights. Now, it sounds like each time you try to put them together, they start going after each other...just not to the extent of a tornado since you are (rightly) intervening. At this point it is a judgement call. You have a better idea of how they are acting when put together. Does it seem like they have potential? Or does it seem like they are just waiting to get into a fight?
If you think they are showing progress with what you've been doing, then feel free to keep it up each day. If you think things are getting worse, then it may be time to separate them completely (sight and smell) for a couple weeks and then trying for a do-over. If you think they aren't getting better or worse, then it's your call. Go with your gut.
It could be that they would do well in side-by side pens for a while without any face-to-face. (similar to what is described above by Mariam). From there, they could then move on to regular meetups again. If you feel they need to be completely separated first, then after that 2 week separation, you could start the side-by-side pens and then move on from there.
If you are working with a rescue, I would keep them in the loop. If it ends up that the two ultimately won't get along, then the rescue typically will allow an exchange. Sometimes, through no fault of yours, two rabbits simply won't get along.
