Are fossil fuels really formed from fossils?
Let's look at this. A very large number of points for one question.

First, the solar system. We do not see any hydrocarbons in the inner solar system (Mercury to Mars). This is because in this region of the solar system, dissociation by solar UV rapidly destroys primordial hydrocarbons.  This effect is much weaker further out.

Oil well 'replenishment' will happen to some degree over several decades, just from internal migration of oil. Typically only a certain percentage of oil in place is recovered, with the rest left in isolated pockets by the water flood. Give it a few decades and these oil pockets will tend to remigrate and link up, giving the appearance of replenishment.

I'm not sure what you comment of The source of methane way too deep to come from fossils. No fossils involved.. That's an unreferenced assertion.

Helium is present in Natural Gas as a result of accumulation of alpha-decay particles from radioactive isotopes; we can see this from the massive enrichment of Helium-4 over Helium-3. It's not a paradox; geological structures that can trap methane will also trap helium.

The current theory behind petroleum geology is that source rocks with a high organic content (often containing biological hydrocarbons from algae and leaf waxes) are buried in sedimentary basins; at temperatures around 100-150 degrees C this kerogen breaks down to form crude oils (this is verified in the lab). Oil then migrates out of this source rock; if it encounters a trapping geological structure, which need not be sedimentary, then it accumulates as an oil deposit. Gas is similar, with a wider range of source rocks.

The physics of how this happens are well known and established.

I would also note that we don't see hydrocarbons coming out of mantle-derived volcanoes such as at Hawaii. This is a major problem for any theory of primordial hydrocarbons.

Additional Points

First, it would be nice if you provided references rather than a link to a book to buy. 


If hydrocarbons were primordial, then we would expect to find them mostly in areas where the mantle or mantle taps reach the surface - mid ocean ridges, and ocean island volcanoes. We don't. The major oil fields are located in continental extensional basin settings. 
There is plenty of evidence for mantle outgassing - including all volatile species such as hydrocarbons - in the first few hundred million years. Furthermore, on geological timescales the mantle is still undergoing vigorous convection and can be considered liquid.
Is irrelevant.
This is simply wrong, if referring to pores that can offer any support against pressure. The crust becomes ductile at about 10-15km, and the mantle at 60+km, meaning that conventional porosity cannot exist. 
See (1). For the Earth, outgassing was essentially completed billions of years ago, as we can see from isotopic evidence (and I suspect that the moon-forming impact didn't help).