Can copies of the spouses diary be used as evidence in court, for the divorce, and/or for a case against her lover for alienation of affection and criminal conversation? Can email be used if the email is found from the home computer? Of course both will have been taken without asking for consent from the spouse.

Yes, those types of evidence, if legally obtained, can be used in court. The legal way to obtain these documents is through the discovery process.

I also, have a digital recording of myself, my wife, and the third party discussing the affair. During the conversation he admits to inviting her to his place even after he knew I had discovered what was going on and that I expected it to stop so we could have time to go see a councilor. Do I need to preserve the digital recording or can I transcribe it into my journal and it still be used as evidence in both cases? I only ask because the digital recorder is full and I plan to continue using it until this is resolved.

I would save the recording as it will be more useful in court that an transcription.