These teeth will fall out, so no worry there. If the chewing stops, the brown spots may wear off in time, but the teeth will probably fall out beforehand.

There is no guarantee one way or another if his adult teeth will be brown, but it will be totally unrelated to the baby teeth being brown.

It sounds like the dog wants out of his crate; and at his age, he shouldn't have to be crated all day. Crating is primarily to keep him from hurting himself and from getting into other things. You don't say how long you leave him there, but if it's for any extended amount of time, it's not surprising that he's trying to claw his way out.

A puppy needs some freedom, and other, appropriate things to chew on. Pick up some chew toys that deliver their own reward, for example where there are treats inside the chew toy that he can wrestle out, or a place for peanut butter or cheese--check with a pet store. They should help occupy him and focus his chew energy on an appropriate object. Spend more time with him, take him on walks, play fetch, use his energy and give him a reason to be good.

He also needs some training, which requires a time commitment from you and/or other family members, and patience. You can find good training DVD's online. I like Linda White's PuppySmarts, especially if you don't have a lot of time to devote, and Karen Pryor's Clicker Training method.

If he has to be alone for long periods of time during the day, set up a kitchen or laundry room where he can be gated or locked in, with toys, water, etc. If he doesn't get walked during the day, be sure you leave puppy pads, or newspaper, or some acceptable place for him to take of business.

By the way, it's great that you're starting to brush his teeth as a pup, because he will better tolerate it all his adult life. If he hates it, try doing it more frequently, but for less time, just initially. In other words, get him in a calm spot, pet him, put the toothbrush in his mouth without toothpaste, then give a quick brush, for just a second or two, remove the toothbrush, praise him like crazy and give him a treat. Repeat that performance 5 or 6 times a week, increasing the time the toothbrush is in his mouth. When he gets used to that, add a small amount of toothpaste, and go back to keeping the brush in his mouth for just a second or two, Praise, treats, etc. Build up the amount of time he'll tolerate the toothbrush with the paste. Then you can reduce the full time sessions to three times per week, although of course, daily brushing is better. If he still resists the brush, you can try the same routine with dental wipes.

Remember, what he wants more than anything is to spend time with you!

Let me know how it goes.