I have issues with maintenance and engineering spaces.
What stats should I shoot for with regards to failure rates and MSP amounts? Do you always supply enough MSP to equal the deployment time?
You should be looking at your overall maintenance life instead of failure rates or MSP stores. I generally put maintenance life higher than deployment time. As a general rule of thumb I try to keep around 1 engineering space for every 1000-1500 tons of ship, so for you would be 41-62 engineering spaces. Although generally I like to keep around 2 years of deployment time for warships, not 5 years, in order to bring life support requirements way down and reduce the overall tonnage by a bit.
Now, my nitpicks of the ship;
1) Far to heavily armored while light on the shields. Ships of this size benefit more from stacking shields than they do armor. I'd at the very least double your shields while dropping armor by at least 10 (preferably by 20).
2) Far to lightly armed. Where are all the weapons? While on paper the lasers should be enough, generally you should be future proofing ships of this size with more defensive and secondary armaments. Missiles in reduced size launchers are very nice for giving a big extra punch for little extra tonnage. And I'd prefer using more gauss of smaller size compared to a 4x6t turret as at that point making something that large track something that fast is just a waste and inefficient use of tonnage. And then you should have other secondary weapons that fire every increment at a good range in order to deal with larger numbers of smaller ships. Also, CIWS systems on a ship this size is always a good idea (even if its just 2-4 of them)
3) You lack adequate sensors and fire control. The FC controlling your main gun should push its "max range" about 50% further than the max range of your weapons, to ensure that you can still hit targets out at the weapons' limits. You also lack main sensor capabilities. While you could use a dedicated sensor ship to bring your overall sensor size down, ships of this size should be more than capable of defending themselves solo, but without active sensors it outright can't (unless you run a complicated multi-stage missile launcher setup with mines, buoys, etc).
4) You lack fuel capability. For a ship this size and with a deployment that long, you really should have a lot more range than that. Even if you run support tankers to supplement it, the ship should have enough to limp home alone without a fleet.
5) To long deployment. At that point, you're just wasting tonnage on life support systems and inflating your crew requirements.
6) Separate your reactor into a few smaller reactors. One lucky hit with a messon and your entire ship will go boom.
About the armor, perhaps you guys could enlighten me as to how it works? I see the weapon signatures on the wiki, but how does that relate to armor? Does armor have a depreciating value?
Like others have said, the value you set is its raw thickness. The number right next to it is the surface area of the armor belt, which effects the chances of a round that impacts to where it hits on the ship. Notice how this number does not increase linearly with ship tonnage, it increases at in an exponential inverse . Coupling that with the fact that the weight of your armor is a function of its "width" and thickness, this means armor thickness weighs less per total thickness the larger your ship gets.
However, as I stated in my #1 nitpick of your ship; shields are far more valuable to a ship of this size than armor is. Despite armor getting more efficient with ship size they still weigh an absolute metric ****ton and once they get damaged they are basically useless dead weight until you get the ship all the way back to the shipyard for repairs, and add on the potential shock damage you will take from heavy hits which damage your ship through armor even if it has yet to be breached. Shields on the other hand constantly recharge their strength and completely absorb shock damage while they're still up. With enough shields, you can essentially absorb damage without your shield strength actually dropping. This is a function between your total shield strength multiplied by 5 then divided by your recharge. With your current shields, you can take 3.3 damage a turn without them dropping. However, when you double your shields you get 6.6 protection a turn. Here is where the efficiency comes in; Say you take 100 damage from an alpha (firing all weapons at the same time) every 20 seconds. Every alpha, your 200 protection shields have a net loss of 86 damage per alpha (21 damage a turn). Meanwhile, the doubled strength shields being hit with the same alpha have a net loss of 73 damage per alpha (18 per turn). This means your original shields will fall and you'll start taking hull damage in 10 turns, however the doubled strength shields will fall and you'll start taking hull damage in 23 turns. Now, if we triple the original shields instead, you'll only be taking 60 damage per alpha (15 per turn) and you're shields will take 40 turns to fall. So for 3x the weight you get 4x the protection.
Now, my personal preference is to have around 5-10 percent of your tonnage in large ships dedicated to shielding. 10% of 62000 tons is 6200, divide that by 50 tons (weight of shield) and you get 124 shields. Now, look at that; that is the 3x your current value, just like my last example above.