1) Mud Slap for sure. It has a lot higher DPS and will outperform Rock Smash even when Rock Smash has super effective bonus and Mud Slap doesn't. There's really no scenario in which Rock Smash would be better.
2) Stone Edge for defense for better coverage and for offense I think both are equally good depending on situation. You might want to have one of both for offense if you're really pushing it but If you'd just have to choose one overall I'd say that Stone Edge is better. Earthquake does slightly more damage but it has longer cooldown as well making it harder to dodge incoming attacks when using Earthquake.
3) Not really. You already have a level 30 Rhydon with great moveset. Even if it has low IV's, the level 23 one would be only marginally better (that one doesn't have very high IV's either). Your Rhydon squad looks fine as it is for now, that should be enough to choose from for almost every situation. I myself don't use Rhydon much because I usually have a better Pokémon to use anyway, so because of that I wouldn't recommend powering up more of them for you unless you get one with high IV's and good moveset.
4) Not really.
Tips against Gyarados:
Well, Gyarados has double weakness against electric, so Jolteon is going to destroy any Gyarados pretty easily. Gyarados does have a pretty weak quick move for defense so I don't think beating Gyarados should be a big problem. Problem with Rock is that even though it does super effective damage against Flying type, Water attacks (Gyarados' Hydro Pump) will also be super effective against Rock. For that reason I'd say that either use an Electric type or just one of your otherwise strongest attackers (Dragonite, Vaporeon or even Snorlax).