In my opinion for giraffe necks, I think of an example my teacher gave while giving a bones lesson. He said, if he attached a weight on your arm at a high pressure, your bone would accommodate to the weight in time and make changes necessary. The bone would reform in a way that dipped down as the body adapts to the change (this would occur in time, of course). And then, if you reproduced with this bone change, it would be passed down to your offspring.
This is a wholly incorrect understanding. Your teacher should be fired for putting forth an idea that was disproven a century ago. This is the concept of acquired characteristics: that features developed or enhanced during an individuals life would be transmitted to their offspring. Even Darwin considered it to be a possible mechanism for producing variation in individuals. However it is now known to be wrong. There is no means by which the germ cells (eggs and sperm) can be modified by changes to the somatic cells (the rest of the cells in the body).
I think if you have such a flawed understanding of the basics of evolution that it is not surprising you think is has errors or gaps in it. Please continue your study of the subject in an effort to remove these faulty ideas. I think then you will find many of the objections you raise simply vanish.
Although I am entirely new to this forum it seems that there are some (but by no means all) members who are willing to take the time to explain details to people who are genuinely interested in learning. Hang in there, and ask away.
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