I noticed that my gameplan has a FB dive play as an option on 3rd and long but I don't want that play to ever be called. Short of removing all inside runs or all plays of that particular formation, is there a way to keep just that particular play from being called?

yes go to Gameplanning then go to OFF Plays then go to INSIDE RUN then find the FB DIVE then uncheck the box on that play and it shouldnt be called ever

But I want that play to be ran on 2nd or short, or 3rd and short, just not on 3rd and long.

only thing i can think of is you would have to make a RULE where it runs only on those situations or you would have to go into the offensive gameplan and maybe go into the TEXT part of it and make the 2RB and 3 TE be 0 for 3rd and long yet have it at 50 or where it is currently for 2nd and short or 3rd and short

If I do that though it will also get rid of most of my other inside run plays as they use the same formation. I guess I could setup a rule so that it only runs inside run plays on 3rd and long when I'm in a situation that I want to run down the clock.

well then i dont know what to tell you.

You can't rule out a specific play, but you can rule out a specific formation or play type on third and long. If you go into Gameplanning > Offense, you can select Third Down/Long. Then either go into Gameplan and get rid of Inside Run or go into formation and remove the formation of that play. If you want to get more granular with time/score, you'll have to use rules.