I don't know anything about 3D chastity devices. I've never seen one. I can say that it sounds as if your sack didn't shrink, but it distended a bit. Enough to make the device tighter, hence the hurting/pinching. I've had U rings that were too tight on my balls, so I had to custom order one that measured 2 1/4 inches in diameter. That made all the difference in the world.
When 3D printing a cage, can you specify the exact size you want? Measure yourself, if you haven't already. Length hard and soft. Tie a string around your ball sack right at the base, then measure the string. These are important numbers. Use them.
Man, I never thought that I'd be writing about ball sack measuring this evening.

Good luck!