My son had similar night terrors at around 2 1/2 years old with crying and whimpering. A few times, he would scream out (very scary to see and hear). My hubby or I would go into his room and not fully wake him up; rather, we'd hug him, stroke his head, and tell him that "it's okay, we're here" or something else to comfort and calm him. Our pediatrician told us to wake him up fully to comfort him but some nights, he did calm down quickly on his own and go right to sleep again, esp. after a few minutes of hugs. At 3 1/2 now, we don't get them too often but I hear they're very common with active toddlers. I don't know if you can make them pass quicker, but it sounds like you're doing everything you can to comfort him and let him know you're there for him.