First of all, I have a 16 year old daughter with Down Syndrome. She was born when I was 32 years old. I had all the regular testing suggested at the time, and we were not aware that she had Down Syndrome until she was born. She is my second child. When I was pregnant with my 3rd child, I did have an amnio. The procedure itself was fairly simple, and she was fine. I did not have any complications from having the amnio, and the discomfort was minimal.
I know you say you do not really want to have the amnio as you would not change what is, but there are some genetic disorders that would suggest that natural birth might harm the baby further. In babies with spinabifida, some have an opening in the spine and the spine is exposed. If you were to deliver natural, the baby could be harmed by the process. I think you need to do exactly what you are doing, becoming well educated about the procedures, etc. You need to trust your heart, but you also need to trust your doctor.
When My sister-in-law was pregnant with her 2nd child, the AFP test came back very low which suggested Down Syndrome. Keep in mind her daughter is 18 now. The AFP at the time was only double screened not triple screened, and the test itself was not really designed to show Down Syndrome. She had the amnio, and the results of that showed that the baby was okay, and she was fine. Test have come a long way, I am sure, and they have new tests that they didn't have when my daughter was born.
Genetic disorders are not all hereditary. When I had Kristen, I went to a geneticist in Boston. He indicated that her having Down Syndrome was a "fluke." He indicated that, at that time, they had not confirmed that it was hereditary.
I think you need to try to stay calm and positive. Go through the tests you feel are appropriate for you. You also need to get your rest. Having a full-time job and a 16 month old baby with one on the way, you need to make sure you are taking time for yourself, especially with this added worry and stress. Best of luck.