This was my exact scenario... well almost. I got my two bunnies at 6 weeks of age, and was told that they were both boys. Not knowing anything about rabbits I decided to get two so that they would keep each other company. However, I had learned (after having them with my for one week) that they would begin to fight at 12 weeks of age due to hormones, and must be seperated. I couldn't image it... they snuggled, and loved each other. But like clockwork they did in fact decide that they would start circling and I got nervous and decided that they needed to be seperated. It took one year from then to get them to be friends. But it was pure heck doing it. They fought just like you described. It was awefull. I used the car ride method... and it worked fantastic. However when they were out of the car all things turned hellish again. I would recommend that you do use the car ride method, and most likely there will not be a problem between them so long as the engine is on. Anyways, we tried on and off for weeks at a time through that year. Our final attempt took 8 weeks to achieve. And it was basically just the same thing day in and day out. You have to allow them to work it out. I don't mean let them fight. But keep at it, and when they fight, grab them and force them to snuggle side by side while you stroke them and talk reassuringly to them. Once they settle down again, then let them back up. If they fight you may want to do a car ride and put them back together again afterwards. Depending on your rabbits, it is possible to make friends of them... however, the difficulty often doesn't make it worth it.
Even once my girls were bonded the one would constantly be humping the other. They never fully decided who was boss. So after they were bonded and friends for 6 months... I decided that I just had to adopt a lop boy bunny to add into the mix. The result has been that after much work both girls love the boy, and he loves them as well... but now my girls hate each other. So I would always suggest that you do not get a third bunny. If you decide that your girls will not work out, then I would suggest getting two boys and keeping two couple seperately.
I know exactly what you mean about "if they would just get along they would both have more freedom, and a friend, etc" and how frustrating it is that they just refuse to understand that.
After two years of on and off bonding now I have come to the conclusion that I must re-home one of my girls. I fear for their safety constantly. I would never even consider such a thing, however, I have met a wonderful person whom I trust and know will provide a loving home, with lots of room to run (i.e. no cage) and where my one girl will have her very own boyfriend. It's been such a termoil past 2.5 years... and I wish you MUCH better success that I had.
P.S. One thing to note... that if your girls are not spayed they will not be able to bond (most likely). Their hormones will keep them fighting. Spaying, in my opinion, is a must.