Thermodynamics is all about energy.  Are you saying no energy is involved in
metabolism?  Then you probably need to read a basic biology textbook,
particularly the parts on how energy is transferred around a living
organism.

The first thing you need to know is that food Calories are actually
kilocalories -- 1000 of those energy calories.

Biochemistry does indeed involve basically burning those calories
for energy.  Scientists do burn foods in calorimeters, and
things that burn but people can't digest are subtracted.

1000 calories of fat/sugar/protein will differ in how your body
uses or stores the calories depending on its needs, but they
still contain the same amount of potential energy or stored fat.
There are minimal differences in absorbtion and wastage from person
to person, but they're not significant except in cases of diseased
or damaged digestive systems.

As to your question of "prana", since it's a belief "energy" and
not something measurable, there's no way to tell if it exists
much less whether it affects your food.  

Organically grown veggies are not proven to be more nutritious than
not organically-grown ones.  Personally, I avoid organic veggies,
because the popular notion that they don't use pesticides is false.
Organic farms are allowed to, and do use so-called "natural"
pesticides, including copper sulfate, rotenone, and pyrethrum.
Modern commercial organophosphate pesticides break down in several
days of sunlight and water, and typically leave no measurable residue
by harvest.  This cannot be said for the pesticides used by organic
farms.  Organic vegetables that grow at ground level, such as lettuces,
have also been found to be contaminated with E coli bacteria from
improperly cured manure.

In scientific term, burning (as in, producing a flame) is just one of the
form energy liberation can take. The general process is oxidation and
reduction (redox). When you burn something in open air, what you actually do
is oxide the something and reducing the oxygen. For instance, 2H2 + O2 ->
2H20. It's actually a transfer of electrons. The human body relies on a
number of redox reaction to use the energy from nutriments. The calorimeter
also relies on a specific redox reaction : combining things with oxygen (aka
burning).

It's not an oversimplification, because it's exactly the same. Burning and
metabolical process are both redox reactions. The first (or is it second?)
thermodynamic principle assess that whatever the chemical path from A to B,
the energy in the system remains the same. This means, there is no creation
or loss of energy, just transfer of it. So, the simple burning path is
energetically equivalent to the complex biological path. If you watch what
goes on with your lung, it's obvious : in goes O2, out goes CO2. All that
complex path actually amounts to burning something with oxygen and rejecting
carbon dioxide.

Yes. Then, they substract stuff the human beings cannot digest (fibers).
This has been calibrated by putting human beings in large calorimeters, not
to burn them, but to measure their metabolism (influx of O2, output of CO2).

Some industrials use a calorimeter, but most recipes are calculated as the
sum of the calories of their base constituants.

Energetically, yes. Not difference whatsoever. Energy is energy. As long as
it can be digested, it's broken down into elementary constituants.

It will just break down the whole mess, until it has stuff it can burn, and
in the end, it will have an equal number of calories.
Note that we're only talking end product and energy! First, breaking down a
simple nutriment will be faster than breaking down a mix (especially with
fats, they tend to slow down things quite a bit). The total amount of energy
will be the same, but in the first case it will be available in a short
burst, while in the second it will be over a longer time. Also, our body
uses nutriments for other stuff than energy, like building and repairing
cells. From this point of view, the second case will be better, because the
body needs vitamins and fatty acids available in fat.

There is very little variation there, unless you have a really non standard
body or condition (obesity surgery to shorten the intestine, allergy to some
of the food, diarrhea, anti-sugar drugs, anti-fat drugs...). And even if
there are variations from one person to another, a given person will remain
fairly constant in her assimilation ratio.

No, because the one grown in the rich soil and sunny garden will have more
calories ;) A calorie table is only an average. In gives general orders,
like a tomatoe is rather low in calories, poor in proteins... But the
tomatoe grown in rich soil and high exposure to sun will tend to have a
higher sugar content. Likewise, if it lacked water, it will be more
concentrated and have higher sugar content. That's why wine is better when
it is on the side of the hill that gets the sun and on years that have had a
little dryness in the last weeks before the harvest : higher sugar content,
that will lead to more alcool. During the last year in France, with the very
high temperatures and dryness, some fruits (those that survived) had a 30%
higher sugar content for instance...
This has nothing to do with organic or not. It's just that food used to be a
living thing, and as such it has individual variations and depends on its
envirronment. If we feed you a sumo diet, you will be more caloric than the
average human being, because you will be fatter.