Rescued puppy

Question
My husband and I adopted a puppy from a rescue. She is a shy dog- usually warms up to people, loves other dogs but scared of plastic bags, loud noises, walking near a dumpster. These things we are dealing with. However, we are having 3 problems with her and would love any advice you have.
1. She vomits whenever we take her in the car. We've tried doing short car trips but even those make her sick. We've tried crating her in the car, just contains the vomit. Any suggestions or startegies? We'll try anything!
2. We have been working on crate training since she was 12 weeks old and she still barks and cries whenever she goes in her crate. It is now only for 5-10 minutes but is there any way to make that stop? She goes in willingly with the cue of "bed time" but cries once inside.
3. She has started peeing on the floor. For weeks we were accident free and recently she has had accidents once a day. Is there something that could be wrong with her? She can hold it in her crate ALL night and 5-6 hours during the day, however, when she is out she doesn't seem to be able to hold it much longer than 2 hours.

Thank you for any advice.

Answer
Often puppies, even ones from ''reputable breeders'' don't get the early socialization they need.  Youcan deal withthose issues, but it will take a while.  

1  This could be stress from fear.  Try building her confidence.  Start with obedience training. The key to most behavior problems is approaching things using the dog's natural instincts. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at http://www.dogsbestfriend.com/ As you praise the dog for following your commands, it will build its confidence.

Play tug of war with the dog and lose. However at the end of the game, take the rope or toy and put it up, less the dog becomes confused about who is top dog. Ropes from the pets' store quickly turn to hazardous shreds. Ones I made lasted much better. Go to a hardware or home center that sells rope by the foot. Buy 2' of 3/4" poly rope. Melt the ends, and tie knots in it. Get them as tight as possible, put it in a vise and pound it with a hammer. Watch carefully, and be ready to discard when it comes apart.

2 I have never had much luck with the old clock or radio tricks. What I do is lay down by the crate like I was going to sleep there. Usually a puppy may fuss a little, but then settle down and go to sleep. Once it is asleep, you can get up and go to bed.

3 One of the reasons crating works so well is that it inhibits activity.  The dog may be happier in its den than loose in the house. It relaxes, it feels safe in its den. It rests, the body slows down reducing the need for water and relieving its self.  Once out of the crate, activity goes up followed by needing to urinate.  Take her out as soon as you let her out of the crate.  Later, if she quits playing and starts running around sniffing, she needs to go out.  I try to follow the puppy's schudle, but at that age,you may have to decide it has been too long and take her out even if showing no sign of it.