Chopping down trees to make room for wind farms is certainly dumb. If you take a closer look that is yet another story about the dangers of subsidies.

"nuclear fuel is 2 million times more energy dense than any other fuel"

Citation needed. Also i don't think energy densitiy is what we are looking for here. Remember the thorium car? A drop of water (in principle) also contains all the energy needed to power a car for years. Now if you could just get the H-atoms to fuse... The point is, it matters how much energy you can (efficiently, at all, ...) get out of it.

"How can we factor in" - Calculate it.

"We should count not just (...) CO2 during operation, but also (...)"

Yes, PLEASE make a complete calculation based on solid numbers taking every aspect of the whole lifecycle of a power plant into account INCLUDING fuel production, fuel transportation and waste management. The publish it please.