Perhaps it would be prudent to disable acid rain or at least nerf it until construction comes in? Even then, I don't know how well a tent or anything crafted out of wood would hold up against acid.
Could you change the effects of radios? Without NPCs they're basically amplifier fodder and free batteries. Say... an old station is on auto-broadcast or a couple of survivors banded together and put together some radio equipment in hopes that someone is still out there. It would work similar to an MP3 player, albiet slower, and you may occasionally get some random skill experience when they share survival tips and stories. Just because NPCs are disabled doesn't necessarily mean the entire world is empty. You can also modify it to broadcast very loudly in order to attract zombies, then drop it and run away.
Would it be possible to add stone/bone crafting? One of the things I've noticed is that starting in the wild is near impossible due to the inability to create even the most basic tools, particularly knives, water containers, and cooking tools. Oh, and the ability to make string/rope for bows, waterskins, and such. You could also extend butchering a bit, as I've wondered why butchering ants doesn't give any chitin.
I like the gun modification system, so I was hoping you could extend it to clothes and melee weapons as well. Say... sticking chitin plates to your clothes to increase defense while only slightly increasing encumbrance/weight, attaching a taser and discharge system to your gloves for a shocking melee attack, or fusing a gas dispenser and lighter to the end of your weapon and giving it the ability to set enemies on fire at the cost of gas. Also, I found adding modifications so easily is a bit out of place. While silencers are generally no brainers, I'm pretty sure the average joe wouldn't know jack about how to properly apply bullet retools and conversion kits. Failing to add a mod may destroy the mod or add a faulty mod, similar to bionics (Mechanics/Firearms/Weapon skill check?.
Also, about the "Battery consuming mod, perhaps it could work like the UPS does, holding batteries instead of outright destroying them, and being able to power your bionics via battery and powering external items with your internal battery would be a much needed boost to the bionic. Maybe a conversion rate of 20 battery for 1 power and vice versa? On a similar note, you could add "external" bionics like Power Fists and Movement Augmenting Boots which can run off internal batteries without needing to be installed. Then again, that's why we have the UPS I suppose.
A few more craftable ranged weapons would be nice, nothing chemical based of course, crafting gunpowder would be pretty difficult without materials after all. But pneumatic and mechanical weaponry wouldn't be too far our of reach. We have electric motors and gasoline already. A few ranged weapons that could be thrown via the fire key, use the throwing skill, and be properly stacked would be nice.
It might be out of place, but maybe you could add vending machines similar to ones in Metal Saga? We have a money system which is currently unused now that NPCs are out. You could smash one open but it might activate guardbots/manhacks or sound an alarm that will attract zombies in a wide area; depending on what products it dispenses. I suppose you could add security measures to gun shops and liquor stores; maybe add a money cost to gas stations too.
Also, any significant attack (20+ damage) that hits should have a chance of knocking a weapon out of your hand (Str/Dex vs weight check?).
Here are a few new zombie ideas:
Smoker: Moderately tougher than regular zombies. Smokers constantly exude heavy smoke in a 3X3 area. Their main function is to hide groups of zombies from players with ranged weapons. Getting into melee range with a smoker means you'll start taking smoke damage unless you have some form of protection. When killed they explode into a 5X5 cloud of heavy smoke.
Charger: Slower than a regular zombie, but much tougher. They're covered in chitin plates, which grants them significant resistance to bullets. While they may move slow. If a target is 3 or less tiles away in a cardinal direction, they can charge into the target, covering the distance instantly and knocking the target (and anything in between) away a few spaces.
Lasher: Lasher arms have been replaced by long tentacle-esque limbs. They're more vulnerable than regular zombies. They can strike you with a ranged attack from 5 squares away. At 3 squares they may latch onto your weapon and pull it out of your hands (dropped on the ground, Str/Dex vs weight check?). At melee range, they can use a "Bind" attack which keeps you from moving (You can still attack in melee/shoot) and drops your dodging ability significantly until you kill them. Lashers deal much less damage than regular zombies, but cause 3x more pain with their attacks.
Bone Horror: Bone Horrors have bones that extend out of their flesh and mesh together to form a sort of protective armor severely decreasing the effectiveness of bashing and cutting weapons. Bone horrors can pull out long pieces of it and throw them as a sort of spear at a range of 5 tiles. Additionally, at 8 tiles, they can send a spray of small sharp bones that scatter over an area and act like caltrops, damaging anything that steps on them. Attempting to engage a bone horror in melee may cause some damage as the bones cut into you. Fortunately, the same bones that protect them are inflexible and reduces their speed significantly.
Phage: Phages are little more than a giant mass of living flesh. They are extremely resistant to all types of conventional weaponry, as they will only destroy a portion of it and the rest will continue moving. Phages can grow in size and strength by consuming organic materials. Finally, when a phage reaches a certain size, a portion of it will split off, becoming a new, independent monster; this also has a chance of happening whenever you hit it. Phage speed depends on their size, the bigger they are, the slower they move.
Also, since XE037 seeped into the groundwater, shouldn't there be a chance that a killed animal will be resurrected as a zombified version of itself? Or are non-human mammals considered "subprime" lifeforms and die when they catch it?
Last thing, I noticed that the order you place weapon mods in has a minor effect on the weapon's stats. I have an M4A1 with a Battle rifle conversion, .22 caliber retool, barrel extension, and a gyroscopic stabilizer. If I place the stabilizer before everything else, it can hold 33 bullets instead of 32.