I don't want to interfere with the expert advice given, but I have a dog that had the same problem, and she eventually grew out of it. She would be in the car a matter of minutes before starting to whine and drool, and make those tell-tale noises, and would puke consistently throughout the trip. Part of it, I think, was anxiety, as she tended to be an anxious dog anyway, plus she has horrible balance in the car. At the time, we dealt with it by not taking her places that she didn't HAVE to go, because she would have to be medicated, with either gravol or atravet, which in turn resulted in a confused, groggy dog for a long while post-trip. Last time she had it was when she had to fly for moving.
While she's grown out of the carsickness without being medicated, she's retained a lot of her anxiety for car trips unless she's been walked into near exhaustion before hand. I suspect that similar things might be at play with your dog, given your mention of separation anxiety (mine's a bit like this as well ).
My dog DID however adjust recently when I had to start leaving her for ten hours a day after a job change that required me to commute, and definitely was not a job I can take a dog to, so I had no other choice. As worried as I was, SHE was fine. Out of curiosity, how do you know that she barks incessantly after being left alone....have neighbours complained? Has she destroyed stuff in the apartment? Some dogs can be true drama queens and kick up the biggest of stinks until their owners are out of earshot, and then settle down. I think it's good to have a little space sometimes, and lets them learn how to comfort themselves. Are you in an area that has doggie daycare ?
I think it is great that you can take your dog to work, and I agree that they gotta get used to the car at some point, otherwise vet / kennel / etc visits are a nightmare. I'd advocate though, for not medicating an animal just so you can take them with you daily, if alternatives are possible. Taking her with you under those circumstances is just doing more to quell your anxiety, rather than hers.
Hope the homeopathics work for you though