Arkeis' Gyarados is probobally one of their best, but they do suck. A lot of people use pokemonelite2000 or something for straight up sprites.
And that set is pretty fail... to get by Skarmory it's much better to just run a Taunt set and laugh when it can't do anything while you set up. Gyarados' special attack is so bad that there really isn't much point in using it. DD + Waterfall does fine damage to Scizor who really can't hurt you anyway. And all those counters will kill you as you Toxic them, meaning you traded your Gyarados to poison a pokemon with big defenses and the ability to heal themselves. And in SUicune's case, usually the ability to Rest off the stuatus anyway. Substitue scouting works great on Gyarados, however. There's somewhat potential, but a more focused set is probobally better. Sub/Toxic is probobally the best thing your set has going for it. Oh and you are totally walled by Dragons, some of which are designed to kill you (T-bolt Latias).
So you can either go with a Sweeper Gyarados, or a Bulky (Maybe ResTalk) Gyarados.
For the sweeper, I use:
Gyarados @Leftovers/Life Orb
Jolly // Intimidate
88 HP/252 Atk/168 Spe
~Taunt/Subsitute/Stone Edge/Ice Fange/Toxic?
This Gyarados can outspeed any Jolteon after a DD (meaning that you don't have to predict with EQ anymore!) because of the Jolly nature and the 168 EV's. 252 Atk is next, to max out power, with the rest in HP for some extra padding. The choice of item is hard; Life Orb has more power (And it has a chance of 1HKOing Zapdos after a boost) while leftovers helps with switching and setting up. If you choose Life Orb, go ahead and go with Stone Edge or Ice Fang, while if you use leftovers it's better to go with a support move. It also happens that the 88 HP EV's hit an optimum leftovers number. Waterfall/EQ is the best coverage Gyarados can get in two moves, although it leaves you powerless against a Salamence or Latias. Oh and Toxic was just because theoretically, if you use Toxic the first time you switch in, you can weaken your counter signifigantly. That's actually a good idea on your set, so it's a n option if you feel like that was working out for you. Sub works in a similar way, because instead of poisoning your counter, you get a free hit on it, which can be just as devastating, especially for SR weak things like Zapdos and Salamence.
For Bulky Gyarados, use:
Impish // Intimidate
216 HP/64 Atk/184 Defence/44 Spe
~Ice Fang/Stone Edge/Fire Fange/Earthquake
Credit to Kingdrom for the set. Gyarados makes a fine defender due to his typing and Intimidate. He can counter a whole range of attackers, from Outrage Salamence to Swords Dance Lucario. The HP gets a lefties number +1, meaning you can switch into stealth rocks 5 times. The Spe EV's beat something signifigant, but I don't remember exactly what... 184 defence is also signifigant, I'm fairly certain it's to survive a Salamence's outrage after Intimidate iirc. The Atk EV's (iirc) are a guraunteed 1HKO on Salamence with Ice Fang. I will check all these with a calculator in a bit, just to be sure. Or maybe Kingdrom will come in and explain this better than I ever could! Ice Fang is for Salamence, EQ is for Lucario... although in Lucario's case Waterfall does big damage after a defence drop from Close Combat anyway, so Ice Fang or Stone Edge is recommended. Fire Fang is even an option to be a great Scizor counter, but again, like Earthquake, this leaves you helpless against Dragons.
Hope this helps!