OK, here's a question for all of you chummers: Crystal Spine says it doesn't stack with any magical, technological, or chemical enhancement, but Lightning Reflexes is not any of those. It's completely 100% natural.

With the above said, what would be your ruling on this? Would they stack?

There might be some wiggle room in the Crystal Spine description (don't have FA), but Lightning Reflexes "is not cumulative with any other initiative enhancement, be it technological, chemical, or magical". So I would say no.

But Lightning Reflexes is none of the above. It is completely and utterly natural.

The "not cumulative with any other" restriction is also part of Lightning Reflexes, not just Crystal Spine.

Crystal Spine asks "is that other stuff technological, chemical, or magical?", which may be debatable, but Lightning Reflexes asks the same question about Crystal Spine, and in that case the answer is a clear "yes".

My copy of Forbidden Arcana says, "This initiative bonus does not stack with any other initiative enhancement, whether it’s magical, chemical, or mundane." (Emphasis added.)

I would include Lightning Reflexes under the "mundane" category, so by the rules as written, I would say no.

However, as a GM I would say yes. The benefits of Crystal Spine are so modest that they are not in any way imbalanced. 10 karma and 1.0 Essence (and -1 to the Stun and Physical damage tracks) for +1 Armor and +2 Initiative? Not +2 dice, just a straight +2. That won't unbalance anything, even if combined with Lightning Reflexes. As such, if a player were to take Crystal Spine for story reasons then I'd be happy to offer them the fig leaf of +2 initiative.

Sounds like an import of the Indrisa Blood Cobra from Earthdawn, which permanently replaces the user's spine.

Pretty much. And before you ask, there is no crystal which grants thorns poking through the skin

[shudders] SURGE Changelings can occasionally manifest those. Nasty genetic remnants of ancient elven blood magic, passed down through the millennia, just waiting for next cycle of magic to show up again in some very unlucky bastards.

There might be a closer candidate now: Apparently the Xapiri Thëpë occasionally fight against elves with thorns according to Run Faster. (Haven't look it up yet.) Looking back I found this in the Runner's Companion, p.53:

If only one of IE's would fill them in on the Ritual of Thorns, that would answer their questions neatly.