With problems like you describe, its a sure bet that the carbs are messed up somehow. Don't waste money on a new CDI or coils, that wont help. I have NEVER heard of those parts actually going bad on a Ninja 250.
On the Ninja carbs, there are multiple passageways (some hidden). Seems like most people miss one or two when cleaning them. Each and every one must be wired out.
Here is a video of the procedure:
Link to original page on YouTube.
If all else fails, I have an EFI kit I'm trying to unload.