Some really good ideas here.
I do like the idea of a physical chain around door handles / something similar - at a distant glance someone can tell that its going to be a lot harder than just opening door and hopping in. Cons - someone determined will now know to bring more tools. Pros - just making it harder, slowing someone down enough to make it not worthwhile is often enough.
The idea of spray painting batt switch, making it less obvious is very good one. I think on top of that putting small (non descript) cover over it would be good too.
If you put small electric kill switch on it, that can be about the ultimate theft deterrent. Small switch that unless its flipped truck wont run. Now, a determined thief will indeed look around for that, but if you put it in place thats not reachable from drivers seat, maybe not even in the cab at all, the odds of them finding it are about zero (unless they had video of you starting the thing i suppose).
One of the power wires on ecm, maybe THE main power wire on ecm (pin70), if that one is not powered the truck will still crank over, but will NEVER start bc the ecm and therefore injectors arent powered up. Do NOT quote me on that, but i remember chasing this detail around on my mk25, when the ecm shit the bed and i was trying to figure out WTF was wrong (and i didnt have scan tool / cat ET at that time either, which made things a lot harder / made me chase down and try as many mechanical / hands on things as i could).
Put a switch on that wire, put switch somewhere u cant reach from cab, no one is going to find it. Put it outside cab, in spotnear where you grab handles to climb in and out of truck, and you can hit switch as you get in and out with a subtle enough movement that even if someone was watching u start truck they might not even see you do it.
Downsides to that (which my ocd ass would worry about) is the idea of switch being accidentally tripped while truck running, id worry about frying ecm. Lots of electronic things HATE being suddenly switched off while running. Can certainly cause power surges/spikes .... id hate to give these ecms another excuse to pop!!
ONE THING I DONT THINK ANYONE MENTIONED YET, BUT IS ALMOST FREE, AND WOULD STOP 99.9% OF PEOPLE - On the batteries there is a connector between the battery lugs to connect the two batteries... only way to make 24v w two batts. Simple way is to just unbolt one side of the connector so it doesnt touch, make connection. A bit more work is to just unbolt connector and take it with you. The REALLY sneaky thing that almost no one would find (wo a bunch of searching, diagnosing) is to make a FAKE connector.
Might be something like a real connector that has maybe an inch of its electrical core cut out (so it doesnt make electrical connection), with something put in its place to fill in that gap (like fuel line), and big heat shrink put over that so from outside it looks about normal.
Unbolt real connector (only two bolts), bolt fake connector in. Then batts dont actually electrically connect between them = no power to anything. Only a couple mins, need only one wrench
Now, i have two big ass batteries in my box, i hear the .mil trucks run 4 batts, cant remember if its 4 12-volt batts or maybe 4 6-volt batts, whatever, you might need to make two fake connectors to do this on a 4 battery setup (depending on how batts are wired), but still, pretty fast and easy to hook / unhook.
As for fuel cap, it would be easy to fab little locking box to go around outside of cap, keep cap from being removed unless box is unlocked. And make it so box cant be spun around and cap removed that way. Multiple ways to make something to make something that keeps stock cap (so no corrosion issues), but makes it so that you cant easily remove stock cap.
Anyways. Enough rambling, just happened to see this thread and it made a bunch of ideas spark in my lil brain