I believe I've already gone over how the points work.
The way to calculate the next point value for killing an additional enemy is this:
The difference between each subsequent enemy killed is equal to 1000x-500
What this means is that for the first enemy, you will have 500 points. For the second killed, you will get 1500 (2000-500) more points for the next crystal worth 2000 points (500 + 1500). For the third enemy killed, you'll get an additional 2500 points, meaning you'll get 2000 + 2500 = 4500 points.
To get the large crystal values, you just multiple the small crystals by 5. So a large black crystal is just worth 24500 * 5 = 122500. Also note that there are higher value crystals. The Jade crystal is worth 40.5k, with the large one worth 202500. The Moon crystal (which is the largest obtainable crystal) is worth 50k, with the large one being worth 250k

The largest crystal is obtained by killing the correct order of at least 10 enemies, so good luck with that. I've only been able to get 9 enemies before (level 47), using the Hammer.
You actually don't have the correct value for the black crystal in your list. It's worth 24500, not 22500.