Im getting close to the year 1999 and wondering, does the XCom files cults, zombies, monsters, syndicates, mad scientists, etc. content end then and the game switch to more traditional XCom (with final modpack kinda)? Or does the XCom files content continue going on along with UFOs starting to show up more (invasion)?
Yes, you get the Martian aliens in addition to the rest. Enjoy
Almost forgot: unlike the rest, they can infiltrate Earth governments and make the countries stop backing you. Supposedly, Russia is still immune to infiltration.
Worried that I've been too slow tackling the arcs.
If you start 1999 with all the inventions available at the start of vanilla X-COM — Interceptor, Skyranger, Alien Containment, Workshop, Laboratory, Black Ops weapons, HWPs — you are doing fine. Not sure about Stun Rod, but early on it can be replaced by tazers and electric clubs.
If you also have improved Interceptor and Skyranger, improved cannon, dart guns and armour better than Personal Armor, you are doing good. Not sure, if you can get flying suits and weapons with unlimited ammo that early.
ended secret cave missions from spawning (did the research saying goverments/others handling them now)
...
Currently fighting ... random monsters.
Maybe it's the other way around?
and maybe finished the zombie arc (though haven't seen vampires outside of a couple army vs undead battles, so probably still more to go).
Yes, there is more to go, even if it's unfinished
Never seen any of the Shogg content (aside from lantern research) or Cult of the Apocalypse. Though you're listing their completion percentage so low, maybe they're just mentioned here and there in research?
Lantern research should unlock deep cave (Shogg) missions. Not sure if they can appear before the start of invasion.
Cult of the Apocalypse includes "Prison Break" and "Town Cleanup" missions which appeared fairly early for me.
In addition, there are various "Men in Black" missions, which appeared for me around 2002, and the TftD-inspired arc unlocked by researching something from Cult of Dagon.