Adding one more fire control will help with taking out more than one salvo of missiles.
Even better, replace your Gauss turrets with CIWS, which is more tonnage-efficient for point defense and doesn't require a fire control or active sensor.
The downside of CIWS is that it only protects the ship it is mounted on, i.e. it is useless for fleet PD because it will not fire to protect any other ships in the fleet, but for a survey carrier designed to operate alone this is not a problem.
I'd also suggest using only passive sensors, not actives. Active sensors are really only useful if you want to shoot at something, and even if you keep the Gauss turrets instead of installing CIWS you only need a short-range active to detect missiles >5 sec away. Passive sensors are more than sufficient to detect anything close enough to be a threat to the mothership, and no sensor can possibly cover an entire system to protect the parasites anyways so I wouldn't bother trying.
The ELINT module is largely superfluous in my opinion and I would put it on a specialized ship, either another parasite or an unrelated class. ELINT requires finding a population and camping out in orbit over it for a long time to slowly gather intel, which doesn't mesh with the mission profile of a survey carrier which wants to jump into a system, launch a fleet of parasites to survey the system as quickly as possible (ideally <1 year with the right allocation of parasites), and jump out to the next system.
For a similar reason, I'd consider the troop capacity superfluous as you don't want your mothership camping out over a planet waiting for a survey team to finish their job when you could be jumping to another system, and survey-eligible bodies are rare enough (maybe one in every 2-4 systems) that most of the time the troop bay is wasted tonnage (and thus fuel, jump drive size, armor, ...). As ground surveys are rarely time-sensitive, a simple jump-capable light troop transport of 10,000-20,000 ton capacity will do the job and of course you will have these in your auxiliary fleet. I also note that if you intend to carry both GEO and XEN teams, both will be less effective in their roles as you really want a good mass (10k or so) of that unit type on the ground to finish surveys in a quick time. God help you if you also want to tote around CON vehicles... moral of the story: just use a separate transport ship, your life will be so much easier in the long run.
I would consider the non-bridge modules superfluous, although ENG and maybe AUX are not wasted tonnage as much as I don't think you need them. CIC and PFC
are wasted tonnage and crew for what are highly situational modules on an exploration vessel. The hit bonus for your turrets/CIWS from a CIC sounds nice, but you should rarely be in a situation where it is significant and usually the extra 10% bonus to point defense will not make the difference of life or death - either the missile waves are small and you deal with them fairly comfortably, or the missile waves are overwhelming and you're dead anyways. Rarely is there a middle ground. PFC is useless since you don't need the boost to refueling rate for survey fighters/FACs, you will have ample time while traveling between jump points.
Broadly you really want to bring the size of the ship down for two reasons. One: a smaller jump drive (by the way, check that your jump drive matches your
engines, not your ship. A military ship with commercial engines uses a commercial jump drive - save 15% or more on
car insurance maintenance and research with this one easy tip!). Two: get that atrocious maintenance life up to, like, five years or better. You will very quickly want survey fleets that can go on five-year missions or even longer as the galactic map expands and flying home to do overhauls takes longer and longer. The way to do this is to cut out the extraneous components, throw on enough engineering labs to keep things in shape, and then throw in some maintenance storage modules so your parasites have something to draw from while they're in the hangar. I think you can reasonably get a 5k hangar ship down to 15-25k tons with an engine, a hangar, a couple passive sensors, and a bunch of scary-looking CIWS turrets on top to
intimidate the locals provide point defense, exact size depending on component designs.
Second-to-last comment, you want at least two armor layers on any long-range exploration ship you expect to survive
an encounter with the Precursors. Spoilers follow:
Precursor missiles tend to use warheads with damage to penetrate only two layers of armor, thus this will ensure that you do not take internal damage from a stray missile that passes your point defense. Ideally three layers of armor is safer, but two is the minimum.
Last comment:
59,974 tons
Round numbers please.
