Hi, I'd like to help you with your question.
Your son sounds like a wonderful little boy and quite a challenge! Children with personalities such as his often take on leadership roles when they grow up.
It sounds like you and your wife have done a great job of being there for him and helping him with your absences. What you may want to try is some behavioral reinforcements to deal with the acting out at school.
First, develop a method of passing on the responsibility of "caring for Mommy" to your son. Yes, this is a bit chauvinistic in our day and age, but it helps him feel important. Make a big deal of it, like a special medal he wears or some kind of token. Tell him that in order to care for Mom right, he must show his best behavior in all places, home and school.
Try small rewards for good behavior. Before he leaves for school, have his mother remind him that she and Dad are expecting the best behavior and give him a small reward, like a small toy. After school, if he has done well, give him another small reward. If he is good for three days in a row, then take him for ice cream or something similar.
Since he is acting out because he misses you, give him something you feel is special to hold on to for you. It could be anything that he has seen you with before. Remind him to keep it safe and anytime he feels he misses you, he can take it out and look at it. It can also be something small he can carry with him to school.
Along with your contact with him each night on Skype, promise to read to him while you talk with him, if you have the time. Or pick another rewarding activity that he can share with just you, no one else. Tell him you will not do this if he misbehaves in school that day.
Plan a big event for when you get back. Something he loves like a day with Dad at the game and eating out or something else the two of you can do. Remind him of that day as you talk with him.
Eventually, he should learn to deal with his feelings and be able to understand that you will be back to see him.
I hope this has helped you,
You are welcome! I am glad it helped you.