I have known a lot of horses who just cannot handle their manes being pulled - my trainer once referenced it to be similar to brushing your own hair when it's extremely knotty, you don't just pull and rip until you rip hair out because it freakin hurts! Some horses may have thicker skin, higher pain tolerance, etc...who really knows! It might take a lot longer, but I would recommend trying a different method, such as taking a fine toothed comb and back-combing the hair until the uneven or long hairs and left and trimming them. This still gives you a natural look without the stress of pulling! Works everytime!
As for the clippers, I have always used the touch-praise method - have your clippers ready and slowly move them up towards their ears, dragging it along their neck so they know what is coming. The second the horse freaks out, turn off the clippers but stay on that spot. Once calm, turn them back on and feed a small treat. If they allow you to do this calmly, continuing moving up towards the ears and repeat the process when a freak out occurs. I have used this on a couple of horses and it works quite well! Again, it takes a long time, but it will be worth it in the long run!