Can anyone tell me where I can find the proper ruling with regards to an improper substitution in baseball for a base runner? If I stupidly inserted a pinch runner that was not eligible, what’s the call? Is the runner out before a pitch is thrown? Or is the runner disqualified and replaced? I can’t find a ruling for it in the MLB rules…

Under OBR, there's no penalty. Get a valid sub in the game (and the original player has been out of the game, so he can't reenter).

Under FED, it's also an out.