My husband & I did this while I was in graduate school and we will begin again this fall when I start med school. We often use ichat on our computer. With the cameras on we would each study or even watch TV "together". They are not that expensive & at least you can see each other, too.
I know this sounds cold, but you will be so busy that the separation will not be as noticeable as you may think, at least for you. It usually sneaks up on you when you are alone studying and you just wish you had your husband's company or on a weekend that you couldn't visit because you had too much to do. On a daily basis, though, you get into the flow of your classes and you are fine.
As for cheap airfare, my Mom (the queen of cheap airfare) gets e-mail alerts whenever there is a big airfare sale. I think you can get these from individual airlines and through sites like travelocity & priceline. You just have to be ready to buy as soon as you get the alert because the seats fill up fast.