Not sure why you need to do 100 sit ups in one session. If you were doing Biceps Curls for instance, would you do a 100? The abdominal muscles are the same as any other muscle and 3 sets of 12-20 repetitions is sufficient, 2-3 times per week.
As for the ache, you are probably pulling at the back of your neck. As Daffy says, you should just keep your fingers at the side of your ears or temples. Also, your chin should not touch your chest.
Why don't you try some different ab exercises, like crunches on a Fitness ball or weighted crunches, where you have legs outstretched, knees slightly bent, so heels are resting on floor. Hold a medicine ball above your head and raise shoulders off the floor. (You don't need to do full sit up). Hold that position for 3 seconds and then back to start. Make sure you keep the ball above head.
Also, try weighted reverse curls, for lower abs. Grip a lightish ball between ankles, raise legs up, so feet are facing ceiling, then lower the ball slowly towards the floor. You should be lowering the legs from the hips, keep legs static, no bending or straightening at the knees.
One other tip, pull your belly button in towards your spine, when you do ab exercises. This activates your Transversus Abdomini muscles, which are a girdle of deep seated stabilising muscles. Doing this, also when you are walking around, sitting or just in general, works the ab muscles without doing anything. Remember to breathe properly though.