Hey, sorry for the delay. First of all, thanks for playing, and I'm so glad you've enjoyed it!
If I am understanding correctly, you can get a clue to the second warp in the Tuner facility from one of the "generic" (flat texture) NPCs who hang out in the "observation deck" area right outside the spawn in. Of course, not all warps go to different places, so you've probably already accessed the location this one leads to from a different world. I think it leads to the dark / empty version of the desert area. I think the only other portal in the facility is the "normal" one, past the door that unlocks after you pick up the Tuner.
As for the combination lock, I will be the first to admit that the puzzle that guards it is ... unreasonable. To some extent, I guess that was a matter of "artistic vision" winning against good game design. I got pretty enamored with the idea of a "secret area" that was so hard to get to that it might as well be an urban legend ... I am not sure I can say that I "regret" it per se, but I definitely understand the frustration it causes.
Anyways, I think there's actually a thread in this very discussion board, from a couple of years ago, wherein a few folks and myself go into a bit of detail on how to solve it. I think one person actually did. Another person went into the game files and simply removed or opened the door, and frankly I salute them. I think that also counts as solving it, from a meta sort of perspective.
In any case, I think that thread should help, but I can also try to look up the solution in my files.