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Old wells will refill just as do forests, just takes a lot longer.

Old wells won't refill, but new ones will form. In a hundred million years or so, today's organic rich sediment will be new oil fields.

The problem is, we use it far, far faster than it forms. If it was forming at the rate we are using it, and doing so for the past few hundred million years, the oil layer would encircle the whole earth several miles thick.

Depends on if you are talking about oil or hydrocarbons in general. Methane forms very quickly. The problem is it can't exist for more than a very brief time anyplace where there is oxygen present. Being lighter than air it migrates to the upper atmosphere. Methane and oxygen with a little UV and you end up with CO2 and water. So methane is constantly being created at a very fast rate. Unfortunately nature destroys it almost as fast as it forms. The difference, the stuff that gets sequestered away from O2, is what we find in gas fields.

We had a bog by my house that got hit by lightning and the methane escaping from the decomposing plant matter burned for three months. It stuck with me because the trees burned off in the first few days and after that it was just the bubbling water burning. No way to put it out, they just plowed fire breaks and let it burn. Stunk like nothing I can describe, burning bog is a stench all by itself. Yes I know that pure methane has no smell, but the stuff coming out of a bog isn't real pure.

Now that bog is always creating methane. It is just that normally it simply dissipates and is destroyed in the atmosphere rather than burning on the ground where we can see/smell it.