The Lost Lowdown

I'm no wellologist, but would the shaft of the well that Locke fell down be there if the well had not been dug yet?

if he fell all the way to the bottom, then yes. wells dig down into the water table, which is why you can't really just dig a well anywhere.
i am a wellologist (PhD Wellology from the London School of Economics, 1996, Go Fightin Buckets!), and i can tell you that the rope wouldn't be.

I'm not a wellologist, more of a well-enthusiast.

Here's an idea.

Sawyer has his hands on the well rope when the flash happens. We've seen that anything they are touching goes with them. So the rope goes with them to a time before the well, and the orchid are built. How much ever time later, some Dharma person is taking a stroll around the island and notices this rope buried in the ground. Dharma decides to dig a hole to find where the rope goes and eventually they find the donkey wheel. They build a well to the donkey wheel, and eventually, the orchid.

Yeah...I know...major mind-fuck.
(The only reason they can time travel in the first place was because their actions after they started travling led to the discovery of the ability to time travel.)

Speaking of wells...
In a deleted scene from season 4....after Ben leaves the island they show him finding a well about 30 or so feet from where he transported to. Inside a rock in the well there are passports and other items.

Yeh clearly they will dig where they find this rope that Sawyer brought back in time.

Oh and there was a lantern in the ice cave aswell, which Ben used.