Calorie Counting Conundrum

About a week ago, I started using Everyday Health to keep track of what I eat, how much I exercise, and my weight.  It's much more convenient (at least for me) to keep a food journal online than by pen and paper, but I've run into some difficulties.  I cook most of my food at home, myself, and I try not to buy packaged, mass-produced, chemically-engineered food except when I have to.  This makes finding the foods I've eaten on EH's list difficult.  They have all kinds of name-brand varieties of pre-made dinners-- you know, the ones that advertise "Just heat and eat!"-- but more natural ingredients are harder to find, and less specific about their serving sizes.

It's even more difficult when I make my own food.  I recently made pulled pork, including my own barbeque sauce.  When listing this food, I had to settle for "Cripple Creek Pulled Pork" (whatever that is) with generic barbeque sauce, since I had no way of knowing the caloric content of my homemade stuff.

I also have no way of knowing if their calorie values for unbranded food (most of what I buy) are accurate for the specimens I am eating.  For example, the calories in cherry tomatoes are "per item".  My cherry tomatoes may be larger or smaller than those EH bases its calorie values on.  I buy pastured eggs, which have been found to have 1⁄3 less cholesterol, 1⁄4 less saturated fat, 2⁄3 more vitamin A, 2 times more omega-3 fatty acids, 3 times more vitamin E, 7 times more beta carotene, and 4 to 6 times more vitamin D than regular eggs.  So when I'm watching my cholesterol, do I go by the 211mg in a single egg, as EH suggests, or should I go with a third less than that, 141mg?  That's a pretty big difference.

I know, I know.  To resolve these issues, I could consult other online calorie and nutrient counter sites, compare their values, and either choose which one I think is most accurate or take the average.  But the whole point of a site like EH is its convenience in not having to do that.  For now, I'm just estimating based on the EH guidelines, and trying to make sure that my estimates are likely higher than the actual values, so I may be pleasantly surprised someday.

What do you think?  How does one count calories (or any other nutritional content) on food items that don't come in a package?