This thread belongs in the Setup & Repair forum.
Definitely more information needed. Some of these questions may not be relevant, but you weren't specific so I have to ask...
Anyway, when you say painted your bass, did you actually sand and paint the neck or just the body? If you painted the body, did you clean up the neck pocket at all? Is the neck shimmed? Are you sure that the neck was flush with the neck cavity as you screwed it back on? Did you take string height measurements before you removed the strings to determine how much relief there was? If you loosen the truss rod before removing the neck, then how do you know that you tightened it to the exact spot you had originally? Is the neck in a backbow? Now that you changed the string height at the bridge, did you measure that before you modified it (it may help you get the neck close to where it was)?
When a neck is removed and reassembled, the truss rod can take a few days to settle. Well, it can take a few days even after a truss rod adjustment.