Celebrim
Legend
Flint is a stone that's high in Magnesium. The sparks are burning magnesium, not molten iron.
I don't know where you are getting your information, but none of that is true. First, 'flint and steel' only requires a hard sharp rock. It doesn't require flint specifically. Secondly, flint is not actually high in magnesium. It's semi-crystalline silicon dioxide. It might have various trace elements, but it doesn't have a lot of magnesium and doesn't require any magnesium. Thirdly, the mode of action is the same as the grind stone. The impact of the stone with the steel shaves very small particles of iron off of the striker. The mechanical impact is turned to heat, heating the tiny iron shards red hot. These in turn rapidly oxidize, or burn, because of their very high surface area compared to their volume. This releases even more heat, which in turn can ignite highly combustible objects. Paper and light cloth are very much highly combustible objects, for a lot of the same reason that the shards combust so quickly - very high surface area compared to volume. The same reason that just about anything will burn if you aerosolize it.
Getting flames for a char-cloth, "first time, every time" therefore doesn't really impress me. That's what char-cloth is supposed to do. As for lighting wood, except in extreme conditions (desert conditions) you can't even light wood with a match. You can prepare it by shaving it into very fine strips and light that, but if you try to light thicker wood lots of things work against you including the fact that the initial char acts as an impressive heat insulator that protects the wood underneath it.
You can burn yourself, slightly, with the sparks from flint and steel. You get micro-burns on the skin. Look at a machinist's hands and forearms some time.
So I'd consider the damage to be "lethal" on the "less than a hit point" scale.
And there is where we run into the big problem. There are no fractions in D&D. Nothing can do a fraction of a hit point of damage. So when you start scaling things down like this, you hit a point where the best approximation of a small quantity is zero. Those 'micro burns' do no damage. In game terms, the sparks may be lethal or not, but they cannot do damage and cannot start fires or damage anything without (as it stands) DM fiat. If they can start fires by DM fiat, it doesn't matter whether the sparks do lethal damage or not.
As for Non-Lethal Substitution: For spells like Fireball, think Flash-Bang.
Flash bangs do sonic damage; not fire. If you are close enough to them to be hit by the thermal effects, it's very much lethal damage.
For Electrical effects like Lightning Bolt, think TASER.
Tasers can easily kill you. However, the mode of action is not necessarily the same as normal electrical shock. Taser's in fact do little or no non-lethal damage. Like the flash bang, they primarily inflict a status effect. However, if they send you into cardiac arrest, well you won't notice how non-lethal they are.
Cold damage? Thermal shock. (You can knock yourself out by placing ice on your wrists or the back of your neck. )
I presume you mean cold shock physiological response. Thermal shock is a different thing that can be used to destroy objects. And I'm skeptical of your ice on the wrists trick. Cold shock response is usually induced by emersion, and it very much can kill you in the same way the Taser can.
Acid? That one's hard.
As long as we are stretching to try to accommodate the idea, any skin irritant with effects that would go away in hours rather than days. However, I'm not really convinced that any energy damage well corresponds to nonlethal damage.