Jen:

I'm one of those people who got a positive result from low-carbing--around 160 cholesterol now, with HDL and triglycerides both coming in at 70. The current thinking is that a 1:1 ratio of HDL:tri is just wonderful! However, it's just the current thinking, and may be dead wrong. According to Ravnskov and others who have researched the medical literature, there is precious little evidence that cholesterol levels can predict heart disease at all. In women over 65, for instance, the lower the cholesterol levels, the greaterthe risk of heart attack--not a piece of information that the popular press tells us, eh? Most of the cholesterol in your blood is manufactured by your liver, in any case, and does not come from the foods you eat.
Further, no matter what the correlations between any blood work number and any health result, there is no way to know if that number somehow causes the result. Correlation is not causation. In other words, I'd advise you not to fret. If you feel good on LC, stick to it.

As to eggs...if you buy organic eggs from free-range chickens, there is still cholesterol in them, but the ratio of omega 3:6 fatty acids is actually better than the ratio of those fatty acids in farmed salmon! (source: USDA data base) Again, as far as they know now, this ratio can tell you how heart-healthy the fats in any food are. If you continue to worry, you might want to read the new Protein Power Life Plan or Emig for info about healthier fats, but in general, the advice is to eat more vegetable fats (avacados, olive oil) and organic eggs and free-range meat.