Once Salamence/Gyarados gets a Dragon Dance up, its pretty much game over right there, your only answer is hoping that Machamp is in good form, because the rest of your team is going to die from EQ/Fire Blast, they pretty much rip you apart. With Gyarados you will struggle even more, especially if it is carrying EQ/Waterfall, although most run Waterfall/Stone Edge, although the effect will still be the same.
Assuming your Aerodactyl is dead, which they are most of the time, 3 out of 5 pokemon are weak to Ground, and you have only 1 Immunity/Resist, you need to address this, also I don't see Tyranitar helping your team at all, firstly it reduces Infernape's life largely, 16% damage per attack + entry hazards is going to make its life very short, and even allows Scizor to take him on with relative ease. Sand Stream also severely cripples Machamp, who with Substitute and no leftovers, it isn't very good >.>
I can't think of any direct replacements, but you need a Gyarados counter, and change Tyranitar, something like a Choice Scarf Flygon I think would complement your team.
Since Mence is gone, why go for Jolly on ScarfGon? You can just stick with Adamant, since you don't need to worry about speed tying with Jolly +1 Mence anymore, plus you'll get some of those KOs you mentioned missing with Jolly. Also, drop 80 Speed EVs and throw them into HP so you can live a +2 Lucario's ExtremeSpeed/Bullet Punch, which some of them have now just for Tyranitar, which could bite you in the ass since it can also kill of Gengar now.
Do not use Adamant Flygon. Flygon is EXTREMELY popular in suspect, so you want to at least tie with other Flygons.
Do not use Machamp to fight other Machamp. Gengar is amazing against any No Guard Machamp apart from Bullet Punch ripping off 30% of your health, given that Payback doesn't OHKO you on the switch. It's absurd how often people forget the exact wording of No Guard. Hypnosis will always hit.
Why are you using Aerodactyl? Without any SR-weak pokemon, there doesn't seem to be any point to using a lead that literally only Taunts, Rocks, and dies.
I recommend this as your lead.
8 HP / 140 Atk / 144 SpD / 216 Spe
Yes, the EVs serve a purpose.
Against Top 10 Leads of Suspect:
->Azelf: U-Turn to Flygon, (you purposely lose the Speed Tie so Flygon will never be prematurely burned against an aggressive opponent) U-Turn back for a quick KO or a scout.
->Metagross: You survive Meteor Mash 88% of the time (crit kos you, of course). Switch to Machamp and commence ownage.
->Heatran: You survive Fire Blast, Stealth Rock, Taunt as it tries to Stealth Rock expecting an Explosion (unless it already SR'd), Explode or U-Turn.
->Roserade: Taunt, SR. You survive Leaf Storm. Explode or U-Turn.
->Machamp: SR. You survive Payback thanks to the Berry (halves the efficiency of Dark attacks if super-effective). Explode or U-Turn.
->Gliscor: Taunt, SR. It can only use U-Turn.
->Infernape: Flinch, SR. You survive Fake Out + Fire Blast. Use any move from there.
->Forretress: Taunt, U-Turn to Machamp.
->Swampert: Taunt, SR. Explode or U-Turn.
->Jirachi: If it's Scarf, and I advise strongly against sticking around to find out, this is the only lead you lose to in the Top 10.*
*"Winning" for Azelf is setting up Stealth Rock and preventing it on your opponent's behalf.
Later in the game, Azelf is not useless as Aerodactyl is. Usually you'll still have 40% upwards (obviously not if you Explode), so you can keep weaving in and out with U-Turn and the threat of Explosion. Taunt is useful too. You can outspeed other Infernapes to hit them with U-Turn. Although that seems stupid, Azelf's base Attack is 125. It hurts, especially if Infernape's used Close Combat.
Yeah, I really typed that mostly because of the picture, but w/e.
The problems you've listed are pretty easy to fix.
1. Change stone edge on flygon to thunderpunch. I know stone edge is better in general, but unless you want to get swept by gyara, I would want a good revenge killer for it.
2. Take out hypnosis on gengar and slap on explosion. Hypnosis is unrelianle anyway and explosion gives you an option against stall. Explode on bliss behind a sub (they don't see this one coming you see), then as long as you can wear gyara down with ape, empoleon can sweep.
3. At this point, you've patched up some big holes on your team but you're weak to mence (flygon only gets a speed tie). I would personally take out machamp for either a CB scizor or a shuca gross with max HP, max attack. That can serve as your DD mence counter as long as its healthy (over 50%). Gross can also explode on bulky waters, setting up your empoleon sweep. If you make this change, flygon will become more disposable and you can probably change it for a suicune or something, but that's up to you.