Whenever a dog is poops in the crate, you should first assume that the crate is too big, or of your not taking the dog out often enough. Some people place shoe boxes in the crate to make it appear smaller. The dog should only have enough room to stand and turn around. However, in your case it sounds like her was crying BECAUSE he had to poop. I always took Joey out when he cried. I placed him on the pee pad, a rather large one, and waited 3 minutes or so. If he didn't relieve himself, he went back into the crate, and you pretty much have to ignor the cries. Since your dog is older, I wonder if he just isn't use to the crate. By the time Joey was that age, he graduated to sleeping in our bed, with a pee pad on the chest at the foot of the bed.
I found some large rolls of vinyl with soft backing at Jo-anns and we placed that under x-pen. I made some pee pads for Joey, because he never did like the disposable ones that much. It might be helpful, if you blot a little of the pee with the pee pad. Some people keep their dogs in the small crate and take them out every hour or so and place them on the pee pad, if he goes he gets praise, treat and is allowed to play for a little it outside the pen, then back into the crate. I think nighttime is the easier way to learn to use the pee-pad because after 3-4 hours the really have to go, and you place them on the pee pad. The same is true in the morning. I think the first few weeks, he's just adjusting to the new family, and this is probably pretty scary for him being in a totally new environment at this age. This link has some good tips on house traing.
Free House Training for Puppies and Adult Dogs - No More Accidents Starting Today!