I have really been working hard for awhile to develop a nikkyo that doesn't hurt. I have not had a huge amount of success so far.
I had a very interesting conversation with a Hakko ryu practitioner earlier this year. The gentleman showed me that it is possible to lock a joint without causing pain or causing uke to feel much at all. He locked my wrist softly and then rather than continuing to apply pressure, he locked my elbow softly. Again without continuing to apply pressure he took control of my shoulder and I had to go prone on the mat to deal with it.
I am not very good at feeling how much of a lock I have on different uke's joints at this point, so i am trying to figure that part out. I figure at the end of the day it is about drawing energy from one of my heels, letting it spiral up my body and then into uke's body and back down into them....then a bunch of stuff I haven't figured out yet...(step 3 profit).
A couple years ago Ellis Amdur introduced me to the idea that nikkyo is essentially a general shape of energy... a "gathering" movement of energy, as though you are scooping up armsfull of tall grass and bringing them into your belly. Daito ryu seems to have the same kind of thing going on, with Nikkajo being characterized by a certain kind of spiral movement. It would be neat to be able to do this without overt physical movement at all....just, when someone touches you, they sort of get sucked into these grinding gears of ki.
Well, I'll let you know if I ever figure THAT out.
In the meantime, my advice is, pay attention to how much pressure you are applying to the wrist. Learn how to lock the wrist without applying so much pressure that uke feels pain. When you get there, consider how to lock the elbow, also without pain. From there go to the shoulder, or skip the shoulder and go to their center, or skip their shoulder and go to their front foot.