You mention that Salamence is physical but the only physical move it carries is Earthquake. Dragon moves are special and it is more suitable to call that a mixed sweeper, and modify nature and EV's to suit that role. Flamethrower is generally a good move for Salamence, as it destroys Skarmory and Metagross. The remaining Steel types can be dealt with easily with Earthquake. If you want to run one mixed and one physical sweeper, don't run Metagross mixed and Salamence physical, but run Metagross fully phyiscal and Salamence mixed.
252 Atk, 100 Def, 156 HP
-Agility / Shadow Ball / Explosion
Metagross basically only does physical well. It has plenty of coverage and there aren't really any foes for it where special moves would be preferable over its physical power. Perhaps Thunderpunch hits Skarmory a bit harder, but in-game Skarmory isn't a threat to Metagross, it never runs Whirlwind and almost never Spikes, which are the only things it can really do competitively when facing Metagross.
For the last move on Ninjask, Substitute is often used to block foes in between using Protect to rack up more Speed boosts to Baton Pass.
Swampert is a good pokémon, it can do quite a bit. Special walling isn't its speciality but electric immunity makes up a lot. Something like this works:
basically curselax only a bit different.
Swampert can run many sets quite viably, it can also run a more offensively oriented set:
The Dome Ace at the Battle Frontier actually runs this set as well, with Leftovers, and it can beat quite a large number of pokémon. It's good defense lets it handle physical attackers while Mirror Coat takes out special attackers like Starmie. Just avoid grass at all cost. It can't really get around bulky stat boosters though, like Calm Mind Recover Latias, Curselax, etc, because it lacks the ability to recover damage quickly and it lacks the ability to stat boost, which CursePert can.
Master balls are the cheapest thing ever invented. It's more fun catching everything with balls that can fail. 'caught Latios in the wild without master ball ftw'