Sounds strange.
In the FSM, there's a good troubleshooting chart in the Engine Mechanical section. On my '92 books, it's page EM-81 for the 3.0.
There's a section for "Starter runs - engine does not crank", giving Starter or Flywheel or Drive Plate as the choices. I really can't remember if when my starter gave out if it made any noise (i.e. running but not cranking the engine) or what. But the Starter is one of the few things known to give out early on these. It's the only non-suspension or exhaust part I have had to change.
The "no initial combustion" section's top 2 are Distributor or Ignition Circuit.
I wouldn't think your problem would be from remnants of an alarm, but both of my 4runners had parts of aftermarket alarms on them. With the '98, on a no-start issue that sprung up after pulling over to answer a call, I removed all alarm parts I could find. In the end, it was a main fuse or link that came just a tiny bit loose, and re-seating it fixed it. But with that, there was no cranking at all.
(Though if you still have no spark sometimes, maybe there's a fuse or link for that system that is separate from your other electrical stuff....check that before pulling out too much hair)
Good luck