Tell me, how much would be the difference in intellectual prowess between a 99 ranked JEE student and a 100 ranked JEE student?
In my opinion, there is no difference between the intellectual prowess. It is pure luck.
If you want to break into the top 100, hard work is not enough. I'm sorry but its not. You have to be a certified genius. I studied for two years at FIITJEE Noida where a girl regularly topped in every phase test. She had completed her JEE syllabus in class 11 itself. Many of our faculties there had predicted her to finish in the top 10.
Result: Her rank was 378. Not a bad rank, but I certainly expected better from her.
This is why JEE is so tough. No matter how good someone is, there is always someone else better in this vast country of ours.
PS: If you're not a genius, don't fret. Work hard and you might still get into IIT.