Batter rounds first and goes to second for a double, Runner on third scored on hit. Defense appealed batter missing firstbase. Umpired ruled batter out for missing first and runs does not score. Is this correct or should run have counted?

Depends on the situation. If there are two outs, the batter must reach first safely for any run to count. If this were the case, the appeal at first would be the third out and the runner would not have reached first safely, therefore, run doesn't count. In all other situations (at least I can't come up with any), the appeal would have the BR out at first, but the run still scoring.

Where would I find this in the FED rule book?

Don't have much time, but best i can find for you right now is Rule 9, Article 1a. "The third out is made by the batter-runner before he touches first base." Basically, it is saying that the BR must reach first safely. Now, here's an interesting twist on this. Let's say R3, 2 out, ball hit into right field. R3 crosses the plate. BR rounds first and tries for two, but misses the first base bag. He is thrown out at second base. 3 outs, run scores, inning over right? wrong. The defense can still appeal his miss of first base which would give them in theory a "fourth" out. This would disallow the run that scored since the base runner never did reach first safely. I'll look at the book to see if there's anything else for you but that's what I've got as of now.

Thanks, that helps alot.