Cat problems. (really long sorry)

Hi Im new to this website so Im hoping Im posting this in the correct area. Heres alittle backround info before I ask my question.
I have a 8 month old kitten who we found (Zoey). She was around 8 weeks old when we found her. She is fixed but when we found her she had green spray paint all over her. But we've had her now 8 months and we when we left to go to a store or somewhere she looked lonely and just cry. So we recently brought in a new kitten(Peanut). The guy who had him told us he was 8 weeks old with full shots. We relized quickly that he was only 4 weeks old. So we've been hand feeding him. Now at nights because Zoey would sit on our chest while we were sleeping and just pur loudly and this got alittle annoying so we got a really big dog cage to put her in at night. Her foods in there and litter and everything. She loves it and will go into at night before bed. Anyway when we first got Peanut Zoey hissed for a couple days and now shes quieted down but now whenever we let them roam alittle on the floor Peanut wants to play and Zoey wants nothing to do with him and will try and bite his neck. Now Im not sure if shes trying to kill him or not but we've never let it happen to long just in case. She in curious about him but at the same time hates him. But now at night we have to lock the cage door and keep him away from the cage because she will stick her paw out and use her claws. Im seriously going nuts because I would never want to give my babies away not that Im thinking about it either im just seriously at the end of my string. Is there anything I can do to get her to like him? I mean shes not that old hes just really young at almost 6 weeks old (Next week). Any suggestions? Again Im sorry for this being really long.

Sounds like she might be biting the back of his neck to carry him as a mother would.

See I would agree with you but its the side and the front of the neck shes grabbing. (should of added this info)
Which is why its worrying me. If it was the back I would be okay but its always been the side or front. Is she just confused maybe?

My first thought was that she is disciplining him like a mother cat would. He was taken from his mother far too soon and still needs to be socialized. How do they get along otherwise? Has she ever actually hurt him? I would just watch them and not intervene unless she draws blood. Yes, he's going to squeak, but it doesn't mean she's killing him. If you're concerned about her using her claws you need to start clipping them, or using something like softpaws. It would be a good idea to start clipping Peanut's claws, too.

Have you read the article about introducing cats? You may need to separate them for a time and start over with the introduction.

Are you sure he's actually had his shots? Did the person you got him from have vet records showing what he's gotten? Even if he had been 8 weeks old, it's unlikely that he would have had the full series. I first took my kittens to the vet at 6 weeks and he spread the shots out over several weeks because they were too little. They were 12 weeks old before they got the last booster shots.

Uhm they get along alright I mean he wants to play and she wants nothing to do with him so she'll hiss or moan/cry at him. Or when he's sleeping she'll just out of no where pounce on him and either sniff him or bite him.
I've clipped both their nails even though she hates it I still do it. He has no shots what so ever but I did take him to the vet to get tested for Kitty AIDS and all that stuff and they said its all negitive they couldn't give him any shots because he is still too young.
Now after last night I was holding her giving her attention and she was sitting on my lap and she was purring and all of a sudden (no kitten he was down stairs) she bit me and moaned/cried and tried to scratch at me. I think she's starting to dislike me now because I brought the kitten in. She's still showing affection towards my husband but wants nothing to do with me.

Introducing cats does take time (and patience!), and she may well have mixed feelings about the baby. Keep an eye on them, but try to let them work things out - he will only benefit from a substitute mom if she takes on the role (which will undoubtedly involve discipline!)

Read the introducing cats thread suggested above, as it should help you understand what's going on a bit better and give you ideas of how to help the process go more smoothly.