Why is Kairoseki's effect more powerful than the sea? It is said that the Kairoseki is just a solid form of the sea and have the same effect as the sea.

But why does Kairoseki weaken and negate devil fruit's power, like when a DF user is handcuffed or touched by it, it drains their energy and they lose their ability (Logias can't transform when handcuffed).

In case of sea water, I think it just drains their energy but never negates their ability (e.g. Luffy can still stretch to use elephant gun to knock out Kraken).

And is it ever shown or explained where the Kairoseki came from?
Q. It is said that the Kairoseki is just a solid form of the sea and have the same effect as the sea.

Kairoseki is a naturally occurring (though apparently rare) substance that can cancel out Devil Fruit powers and weaken Devil Fruit users. It gives off a wavelength that is the same as the sea itself.


Q. But why does Kairoseki weaken and negate devil fruit's power, like when a DF user is handcuffed or touched by it, it drains their energy and they lose their ability (Logias can't transform when handcuffed).
In case of sea water, I think it just drains their energy but never negates their ability (e.g. Luffy can still stretch to use elephant gun to knock out Kraken).

When comparing two different things, the comparisons should be based on the same terms.
For example, you mentioned that Logia users can't transform when they are handcuffed with Kairoseki, but then, they can't transform when they are in sea either. So this example does not prove that Kairoseki is more powerful than sea.
Next, coming to the Luffy example (Paramecia type).
We know that both Kairoseki and sea weaken Luffy's strength, but we have seen that they do not cancel off his power, i.e. Luffy doesn't have enough strength to use his powers on his own. That is why the strength of his punch weakens when he uses the Elephant gun on Kraken as it goes out of the bubble and makes contact with the sea.
To make it even more clear, I'll give a better example.
When in Arlong park, as Luffy was about to drown in the water, Nojiko had to stretch Luffy's head out in the surface, to try to get him to breathe again. From this it is clear that a DF user (Paramecia type at least) only loses his strength and not his abilities even when under water.
The same way, when handcuffed with Kairoseki, Luffy loses all his strength and is unable to use his abilities by himself. We have not seen any case where someone tried to pull Luffy and was unable to because he was tied to Kairoseki. Thus, there is still a chance that even with the Kairoseki in direct contact with the user, their abilities can be made use of, but by somebody else, and not by the user themselves as they are totally drained out of energy.
Conclusion: This answer doesn't answer the question Why is Kairoseki's effect more powerful than the sea? directly, but rather provides some evidence to show why Kairoseki's effect wouldn't exactly be greater than the effect of sea on a DF user. I used two examples, that of a Logia and a Paramecia type DF user to compare and show the same. Thus the answer would have to be, No, Kairoseki's effect is not more powerful than the sea as we do not have any proper evidence to support such a claim. They both emit the same wavelength and thus, quite fittingly, have the same effect on the DF users.
Update: To support my answer even further, I found an interesting piece of information on the wiki page of Yami Yami no Mi. You can see that (emphasis mine)

The most unique and frightening advantage of the fruit is that the user also has the ability to nullify the powers of other Devil Fruits by simply touching the user and draining them of their abilities. All types of Devil Fruit, be it a Paramecia, Zoan or Logia, are affected by this, though Logias are most affected as they can no longer become intangible by transforming into their respective element. This nullification truly seems absolute, as though the Devil Fruit users had never gained their powers at all. This was shown when Luffy's stretching powers were canceled on touch, unlike the effect of a body of water or seastone, both of which just inhibit a person from controlling their powers. It was shown earlier when Luffy was stuck underwater that his neck could still be stretched above the water's surface, and that Busoushoku Haki would simply nullify the defensive aspects of a Devil Fruit such as intangibility and the malleability of rubber.