What clues are given of the domestic estrangement between John and Elizabeth in The Crucible?
First of all, we are introduced to John separated from Elizabeth, and in one of Miller's digressive notes he remarks,
He is a sinner, a sinner not only against the moral fashion of the time, but against his own vision of decent conduct.
This may have been a piece of foreshadowing for this occurs before we even know of the affair and there is really no greater sin a man can commit to his own soul than to fail to fulfill his duty to a wife.
The domestic estrangement between the two is best demonstrated in a scene that occurs before a scene... it is in the acting directions of Act II.
Proctor can hear his wife singing upstairs putting the children to bed as he comes in late one night from work on the farm. Since she is away from the food, he sniffs it and doesn't like what he smells, so he adds salt before she gets back.
You could take this at face value and say she's just a bad cook. You could see him as over-stepping his bounds. You could look symbolically at salt. John knows his relationship is lacking and is making an effort to re-create flavor.
As they begin talking that evening, Elizabeth's words are forced. He tries to kiss her, but she is not receptive. She keeps her back to him when they talk. They are struggling.