What is your actual situation? If you get free tuition plus a stipend, then normally I would expect box 1 and 5 to be the same, with the stipend on the 1099-MISC in box 3.
If box 5 is more than box 3, that is an indication that you had a scholarship that was more than tuition. Is that true? Was your stipend more than the amount in the 1099? Or, maybe the difference between box 5 and box 1 of the 1098 is a student health fee or insurance, paid by the school that is separate from the stipend? You need to know all this first.
