I've sold my Protege so I can't offer much help.
As you can tell from this thread, my experience with JIC USA wasn't the best one. In the end, they accepted return of my FLTA2's and they issued me a refund. But this was only after about 3 months of a lot of hassle, installation costs, and time. They basically refused to acknowledge there was a problem with the product and insisted I troubleshoot the installation. It was only after they serviced the coilovers, returned them to an authorized shop, and had them re-installed, did they finally grant me a refund after they STILL made the noise.
Back to the topic, to me it is not an acceptable sound, that's why I returned it. Some others might say that it's okay. I wouldn't accept it for a daily driver. The banging noises are loud and obnoxious. For a track car, I suppose it's acceptable because noise comfort usually isn't a top priority. Many other owners of coilovers of various brands have also reported these clunking or banging noises coming from the top mounts of their coilovers. They usually attribute this noise to the metal-to-metal contact from the all-metal (no rubber) top mounts.
After I had the JIC's removed I had Tein S-tech springs and Tokico HP shocks installed. There was an increase in road noise and noise when going over bumps when compared to stock, but only in magnitude and not in quality. These noises are normal, from being lower to the ground, having a more aggressive spring rate, and more aggressiving damping. There were no clunking or banging noises like I had with the JICs, but this is because this configuration utilized the stock upper mounts.
As for the rear camber... excellent question. I don't know about your particular units, cuz you have the FLTA1. But when I received my FLTA2, there were no camber adjustments for the rear. The front has a camber adjustment at the top, but actually that was not intended to align your car. If you notice the markings. I think what it was meant for, was for on-the-fly adjustments to your camber, say for running on the track versus running as a daily driver. For example, you can run slight negative camber for daily driving and then using those top adjustments, run additional negative camber for autocrossing. On the rears, there were no adjustments whatsover.
One solution is to have the bottom bolt holes "slotted"--which means the shop uses a drill to expand the bottom bolt holes in order to align the car properly. I think I was charged about $60 to have the rears slotted, and I never had the fronts slotted but in retrospect that would have been a good idea. By having the fronts slotted as well, you can take advantage of the "on-the-fly" camber adjustment at the top.
Oh yeah and the last thing you probably noticed is that JIC has pretty poor documentation / product support. When I received my units they had no instructions or warranty information.
I wish you the best of luck with your FLTA1 installation. As I said before, the FLTA2 is an amazing product if it didn't have the problems mentioned above. But after my bad experience, I am probably going to switch to a different brand for my next set of aftermarket suspension--maybe Tein.
? 
