Just remember that some umpires may feel threatened by a coach with more rules knowledge than they have... Bringing the rule book to the plate conference will offend some. Known to have a rule book sticking out of your back pocket will "get around". Still just indicating - I don't recall the exact rule number, but I know there's rules that cover umpires formulating grounds rules if the coaches cannot agree shouldn't draw the ire of any umpire (especially one that doesn't want to do the paperwork 
). If the PU has no idea or disagree, you probably have a protestable situation. The only thing not protestable is agreeing to play on a non regulation field, see 1-2-12. BTW: The batters boxes, see 1-2-2 & 2-7-2 - could be considered "agreed upon" if not mentioned before the game.
I think Matt gives you the best advice - report the facts to the AD or assignor of the association that assigned that game (depending on who does that for your school). Having worked for CUI in NC (greater Charlotte area), I know if a coach/AD reports something to the assignor, then we hear about it. Umpires in that group are also expected to file game reports and stuff like you mentioned would need to be in there (except of course the I won't dump someone conversation because the claim will probably be it never happened). If we got to a field and it wasn't lined, put it in the game report. If a coach questioned a ground rule, but we played with it as is or we changed it, put it in the game report. If a coach came out to question a call, put it in the game report. You get the picture I hope - anything that could come back at you later report it so that when/if the assignor does get contacted by a coach/AD he can look it up and go from there. Not all associations are that way from what I hear though.