Since my wisdom teeth are probably coming in what should I do for the soreness in my jaw? I take Ibuprofen and Aleve (naproxen) but what else should I do?

Very little. Besides taking analgesic medications you can make sure the areas where the teeth erupts remain clean and free of food debris. Brush the gums there gently with your tooth brush 2 or 3 times a day. Rinsing with warm salt water can help as well. Avoid chewing hard, crunchy, or sharp foods like chips and crackers back there also. See a dentist for a panoramic xray to make sure they aren't impacted.
Oral surgeon. You should have the wisdom teeth evaluated by an oral surgeon. You may need the teeth removed surgically.