Judging doesn't work like that. By that, I mean, we don't have one guideline every judge follows when they judge a level, or, as you put it "judging standards". Imagine how messy it would be: people following the exact guideline to make sure their level gets the maximum score. Instead, every judge has its own
Judging Style. This is why we have 4 judges per contest! So that judging is more interesting and less biased. So you can't ask to change judging standards like that.
Anyway, the layering problem. It's a recurring problem, one I also had a few times, and there was a way I sometimes managed to fix it: Take the code of all your items that are underwater, and, in the code, cut/paste everything BEFORE the Mario sprite (which should at the beginning of the item part of the code). Leave the water AFTER Mario. That is if you want your items to be behind the water. If you want the opposite, well, switch the codes (water before, items after). That sometimes fixed it for me. Now, if that didn't work, don't worry, judges shouldn't pay too much attention to that, unless it's EVERYWHERE in your level, or unless the judge is very nit-picky (like me, but don't worry, I won't be judging

). Best you can do is leave a note in your entry post in the Vault, pointing out the fact that you tried your darnest to fix it but you still didn't manage to get rid of the layering problems. That way, a judge might be more forgiving (don't count too much on it though).
As for lag, haha. No seriously, I laughed. Lag and loading times are like one of the biggest reasons lose points in contests, and trust me, it IS justified. Remember that we are judging a level from a game, not art, so it has to be fun, entertaining. We don't want to be patient, we want to play the goddamn level. Loading time and lags are annoying. There are some ways you can fix them: For loading time, you could
divide your level in two separate parts (and use
this to get rid of the items that are not visible), or try to remove as much useless items as you can. And tiles, sometimes. One other way to fix loading time (well, not really, it's more like, making it less annoying), is to make your level easier: People won't have to die too often and therefore will not have to load your level several times. Profit! As for the lag, it's easy: just PUT TRANSITIONS REGULARLY. Oh and remove useless items too.
Loading Time is NEVER welcome and it's easy to understand why: if you die over and over, and have to wait every time that the level loads, after a while, it gets very annoying and kills the fun of the level. You could always put a note, again, in your entry post, but trust me, it would be better to try and fix it. But again, it could depend of the judge. If he is a good player, he will die less, and loading time shouldn't be an issue. Same thing if the judge has a good computer (level will load faster).
As for lag, you have absolutely NO EXCUSE, as it is VERY easy to fix. Transitions. They don't kill the mood of the level and are easy to place, add them regularly and you should be safe. A framerate below 20 is VERY ANNOYING to play with (how is it fun to see Mario move a few seconds later after you pressed a key?) (also, you want 15 CONSTANTLY? haha, no thanks), have that in your level and you've got free tickets to lose-some-points-town.
That was a long post, but yeah, I'm pretty sure I didn't forget anything.