Sorry, I guess I missed this, but, does he bark/cry or whatever when you put him to bed, or when he's outside? My dog Josie used to whine everymorning when we kept her in the kitchen. I think she was wanting attention for me to get up. I think maybe it's sort of like a child who had a tantrum looking for attention, if you give it to him, he'll keep doing it.
If it's outside he's barking, you should find out what it is he's barking at, and try distracting him when till the distraction is gone..maybe it will teach him to ignore the distrctions..

Sorry, I didn't read it all 100% :[