====Note this is not my currently used loadout, the current one is further down in the comments====
-Rank: 168
-Size Class: Massive Titan (924 decks)

---Stats (all without buffs, none taking race into account)---
Attack: 2024
Defense: 977
Hull: 5174
Shield: 524
Scan: 201
Cloak: 491
Upkeep: 321.4M
Combat rep: Insane (only got out of Savage yesterday)

---Modules---
-Weapons: 2 Charged Bane Emitters, 1 Crimson Auto-Phaser, 3 Vortul Blast Phasers, 1 Dominion Cannon, 3 Dominion Cannon MKII, 3 Lazuli Mind Controllers, 4 Light Null Rays, Psionic Amplifier.
-Defenses: Auto Evasion Node, 3 BM50 Convoy Shuttles, 1 Dark Complex Thruster, 3 Dark Ring Thrusters.
-Hull: 3 Biomimetic Sealer II, 3 Stabilized Fermionic Armour, 1 Fermionic Armour, 3 Protean Armouries, 2 Vortul Platings.
-Shields: 2 Harvest Shields. (4 Harmonic MegaPulsars in storage)
-Energy: 4 Drannik Power Cores, 1 Dark Energy Core MKIV, 2 F.A.T.H.E.Rs, 4 Isomorphic Repeaters. (2 Dark Energy Core MKIVs in storage, considering to have 2 installed by default rather than just 1, my energy fills up overnight.)
-Scanning: 1 Decryption Quad Frame, 2 Shad'in AI Core.
-Cloaking: 1 Decription Quad Frame, 2 Shad'in AI Cores, 1 Subspace Jammer MKIII, 2 Zolazin Jammers.
-Mission Reward Modules: Omicron Injector, AI SuperComputer, Q-Phase Battery Array, Harmonic Resonator,Thrust Stabilizer, Prototype Mech, Combat Analyzer, Gamma Channeler.

---Resource Production---
2670 Research/Hr (Level 4 Base produces 37.3K/Day)
1790 Minerals/Hr
1381 Artifacts/Hr

The reason I'm asking is because I am one of the leaders in my legion (and possibly one of the more PVP oriented players there) so the newer members usually ask me what to do with their ship, and I don't want to have them follow my example if my own ship is flawed if you know what I mean.

Work on getting Dom cannons MK III instead of Mk II or Mk I---you'll regret those later.
Also, try getting your defense up slightly.
Other than that, I think your ship is progressing nicely. You should get those productions up though, mainly research/mining. You wouldn't have a large need for artis at that level, but don't let it slack. After rank 250+ (maybe 300+), you'll start wanting to get arti up, and if it is extremely low (as mine was) you will regret not raising it previously.

I'll admit myself that those MKIIs were a mistake and do intend on skipping the last MKI to III. Other than that thank you

Right-o.

So you seem to play in every aspect of PvP (Disables/Raids/Hacks), if just a little.

First off, the Drannik Power Cores are considerably less efficient than the Dark Energy Cores. Swap the 4 Drannik Cores for a Dark Energy Core Mk4 and you will get an extra 39 energy, in 3 less decks. A subtle change, perhaps, but it adds up. On the topic of energy, your energy charge:max energy ratio seems kinda low. If you're losing a lot of energy capping then you should install cores to make your energy not quite cap. A good charge time is around 9 hours.

With the light null rays, they aren't really worth it. They're expensive, and offer only the tiniest of boosts. I wouldn't sell them, just install Antiproton 3s (or Heavy Null Rays) in the future. Obviously, sell them when you upgrade. Also on weapons, the Lazuli Mind Controllers aren't particularly efficient deck:attack wise. As you don't have all of your weapons online, which are more efficient, swap the Mind Controllers, as well as the Auto-Phaser, Psionic Amplifier and Charged Bane Emitters (for the same reason) out for researched modules.

On hulls, upgrade all 5 of your researched modules to Perfect Fermionic if you can afford it. Otherwise, don't worry.

As far as shields go, the Harvest Shields aren't so bad, but they're still shields... so they suck. I'd uninstall them, again in favor of researched modules, however, NOT SHIELDS. Shields, as a whole simply just never reach a usable efficiency. The only shield modules I can think of off the top of my head worth installing is the Aegis Capacitor.

Cloak/Scan time. With your future blue badges, I'd buy the CipherBots before the Decryption Quad Frames. Probably more of a personal preference thing though, and once upgraded the DQF are considerably better than the CipherBots. In my honest opinion, you don't need as much scan to hack, either. Elerian or one of the other hackers could probably give you more of an idea as to what benefits scan has in hacking, but for the most part you only really need cloak. Since most of your scan modules are also your cloak modules however, I'd just work on getting some more cloak modules and swapping out. Again, most likely a personal preference thing.

With defense, don't let your defense drop below your decks. That's an absolute baseline, not a target too. As you have spare decks, make sure you start to bring this up.

What race/profession are you?

I realise this is only one rank apart from the original version that I placed on the first page, the one below is just how my ship is right now with the changes suggested implimented.

-Rank: 169
-Size Class: Massive Titan (931 decks)
-Combat Reputation: Insane (524 kills, 191 deaths)
-Race/Profession: Zolazin Saboteur

=--Stats (since I'm no longer working on the daily perspectives medal and have settled with a race, it takes race/profession into account this time)--=
Attack: 2139 (Increased slightly)
Defense: 1383 (Increased roughly 35% over previous loadout)
Hull: 5174 (no change)
Shields: 334 (dropped)
Scan: 101 (dropped, forgot to list that I had 2 stryll hunt sensors last time, since been uninstalled)
Cloaking: 745 (Nearly doubled: Taking Zolazin bonus into account, higher researched cloak module installed)
Upkeep: 365M
Max cargo hold: 900

=-- Modules Installed --=
-Weapons: Cerulean Fighter, 3 Dominion IIs, 1 Dominion I, 1 Heavy Anti-Proton, 4 Light Null Rays, 3 Vortul Blast Phasers.
-Defenses: Auto Evasion Node, 3 BM50 Convoy Shuttles, 1 Dark Complex Thruster, 3 Dark Ring Thrusters, 1 Quantum Overlay Engine.
-Hulls: 3 Biomimetic Sealers (I was dumb with the first one if you're wondering), 3 Protean Armouries, 1 Fermionic Plating, 3 Stabilized Fermionic Platings,
2 Vortul Platings.
-Shields: None.
-Energy: 2 Dark Energy Core IVs, 4 Isomorphic Repeaters, 2 F.A.T.H.E.Rs .
-Scanning: 1 Decryption Quad Frame, 2 Sha'Din AI Cores.
-Cloaking: 1 Decryption Quad Frame, 2 Sha'Din AI Cores, 1 Cloak Field Generator, 2 Zolazin Jammers, Zolazin Race bonus.
-Mission Reward Modules: Omicron Injector, AI SuperComputer, Q-Phase Battery Array, Harmonic Resonator,Thrust Stabilizer, Prototype Mech, Combat Analyzer, Gamma Channeler.

=--Modules in Storage--=
-Weapons: Psionic Amplifier, 3 Lazuli Mind Controllers, 1 Chrimson Auto Phaser, 2 Charges Bane Emmiters.
-Defenses: None.
-Hulls: None.
-Shields: 2 Harvest Shields, 4 T.O Harmonic MegaPulsars (Just a question when it comes to Pulsars, MegaPulsars seem to be more efficient for the deckspace than the more advanced ones, should I stick with these or upgrade to the later ones?)
-Energy: 4 Drannik Cores, 1 Dark Energy Core IV.
-Scanning: 2 Stryll Hunt Sensors.
-Coaking: None.

---Resource Production---
2670 Research/Hr (Level 4 Base produces 81.8k/day. more of the members are becoming loyal)
1790 Minerals/Hr
1394 Artifacts/Hr
(My last scan run didn't turn out well)

-Researched-
Nullrays 2/3
Intra Dimentional Colliding: 0/4
Meta-Chron Fields: 0/3
Cloaking Fields: 1/3
Fermionic Unification: 2/3 <-(Currently working on 3/3)
Quantum Overlay Engine: 1/3
X-Manifold Sensing: 1/3
Stellar Engineering: 0/3
Sub Quantum Logistics: 1/3

What do you think I should research next?

Just saying, your math is a bit off. Vygoid gives +20% research bonus, so you divide by 1.2 to get the actual (unbuffed) research.

Same for the Excavator, divide by 1.1 to get the "unbuffed" artifact.

Proof:
100 * 1.2 (20% buff) = 120
120 * 0.8 = 96 (although only slightly off, it's still not correct)
Whereas: 120/1.2 = 100

Just a tip

I am by no means a mathmetician, but I thought the exact same thing. Good job f3ar3dlegend!