Home Cooked - Will cooking INCREASE kcal?

My head hurts.

As an ex-scientist I find the question interesting! From a pesonal food dairy perspective, I don't worry about it, I doubt it effects my intake as much as say, the inaccuracies on my weighing scales, the scrapings left in the bowl when I serve up, etc etc, but as a science question, hmmm.

No idea though sorry! I suspect it will effect what your body can absorb versus pass straight through you though.

whenever i cook i just log the raw weight of the ingredient.
i think thats the most accurate

for example with pasta
it can be 75g raw
and then between 175-225 once cooked depending on how long you cook it for

so my suggestion is just log the raw food

Cooking food does not change the calories of the food. HOWEVER, cooking food does change the weight of the food. Always measure food raw for calories, because raw weight will be consistent. Cooked weight can vary widely based on actual cooking method, cooking time, specific cooking temperature, final food temperature, carryover cooking, humidity, and other factors.

Example, if I start with 100 game of beef, and cook it 3 different ways, I can end up with 3 pieces of meat a the end that weight 95g, 85g, and 78g. They all have the same number of calories, as the weight difference is due to water weight changes.

Well, technically not so. Different methods of cooking may remove slightly more fat than others. I would think meat in a sausage caseing would retain a little more fat than the same meat removed from the link, then cooked (or if the link was just sliced and then cooked).

Yes, info like this is purely academic, since natural varience in calories, scale increments (and even individual scales might be a little bit off true), 'scraps' in the dish, and more will all play a part on the actual true caloric value of an item. That is why I am consistent with how I measure my food/ingredients (I weigh raw/uncooked), and when my results don't meet expectations, that is when I add more activity or reduce total calorie allowance.

That said, cooking is a chemical change in the food. It has been shown to reduce the amount of some vitamins in some foods, in others (such as asaragus) activates chemicals that make the food more appeasing (to most)... quoting Alton Brown, Age of Asparagus "Now what's really cool about asparagus is that it becomes two completely different vegetables, depending on whether the heat in question is wet or dry. Dry heat tends to emphasize amino acids, which create flavors that are almost meaty. Whereas moist cooking methods bring out the brighter, spring-like grassy flavors, which, I think, is a pretty good place to start.
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If cooking can affect vitamins, it may have some impact, however slight, on how the body can break down and utilize the food, and the energy expended in that effort. While scientists probably have a pretty good idea how this all works and can get us very accurate results, there are just so many different mechanisims involved I don't know if we would ever get a 100% true result anytime soon.