X-rated Bob wrote:
When the relief is correct THEN start looking at the saddle.
+1. That's it.
12-String acoustics usually show a lot of bellying (where the top pulls up into a convex shape thanks to string pressure, raising the action) - even after the guitar has been converted to 6-string. A neck reset helps, but is outside the scope of most home repair (and usually to expensive to have done by a pro). So you have to do whatever you can to compensate at the bridge. Filing the saddle down helps, but sometimes you have to thin down the bridge itself, countersink the pin holes again and possibly make slots from pin holes to saddles to improve the string break angle over the saddle.
If all else fails, cranking up the truss rod so that the neck bows can give you a more playable guitar at the top of the neck at the expense of a completely unusable guitar closer to the body side. Generally you're fighting a losing battle at this point, but it can give you a few more year's use out of the guitar before it implodes.
