My wife and I have been married for 7 years. We just reunited after two yeas of being in separate countries. She has been home for a month when her sister tells her she is invited to Los Angles for an award she won. So my wife went to LA despite my reluctance. While in LA we couldn't keep in touch because she doesn't have a phone and the wifi where they were staying was out so communication was very limited. Long story short when she returned from the 5 day trip a guy that she, her sister and another friend had met at the event sent a email (which goes to her iPhone) to her at 3:30 in the morning to saying how her sweet character had him smiling all day and please come to New York where he is from to visit. He closed with "I hope to see you real soon". When I asked why he sent it at that hour she wanted to try and rationalize it. So my question is does the email itself seem inappropriate or if not the time it was sent at 3:30a.m. and why would he feel comfortable enough to

What time was it where he was? Maybe he just expected it to go to voice mail.
I'm not sure how we can judge on so little. A message like that can be totally innocent or totally an invitation to an affair, or somewhere in between.
Rather than confront her, why not find a time to ask her all about the trip, and try to get in a little mention of hurt over this nice guy who seems sweet on her? She might be much more willing to talk openly if not backed into a corner.
Also... sometimes all couples need a little 'attention' from someone once in a while, just to feel attractive, as long as it stays harmless.
It couldn't hurt to do something sweet and romantic yourself, flowers and candy and dinner and compliments, and say you are jealous and better stay on your toes, and keep it fun and light, as though you are wooing her all over again, and have competition. It might be lagging in your marriage.

Some people just don't think about the time when they do things like that. I have a friend who lives in Nevada and he will send me a text at 3 in the morning my time. It means nothing.

It could be he was flirting with her, but it does not mean she did anything to instigate it.