The Japanese are KNOWN for going "by the book." This could sound bad at first, but actually will end up helping you. The first and foremost thing you need to do is find out how to change your visa status. I think basically going from Student visa to tourist will not be very difficult. It may only require you writing a letter of intent.

I don't think you can have two active visas. You have to abolish one when getting the other. So to get a travelers visa you will be fore-fitting your other visa.

So by going by the book your solution to getting the cheap travel pass could be as simple as requesting the travel visa before you plan on returning to Japan, or just before you leave.

I would STRONGLY suggest going to the Japan Visa page (google search for it) and calling the phone number on the page. They should be very helpful. (obviously you dont need to include the details about the discount pass, just let them know you want to change your visa status before your current visa expires. Make sure to tell them you will be leaving the country for a few days too.)