I just got over the flu. I too had received my flu shot (in October) but was 'lucky' enough to catch one of the strains that is going around and not part of the vaccine. I spoke with my PCP and OB, both of which had me take Tamiflu. Because I got in quickly to PCP, I was able to take this and it helped tremendously with the symptoms. This was the first time I've had the flu in 17+ years, but it was awful until the Tamiflu got into my system.
As for birth defects and such - please stay away from Dr. Google! There are many stories and theories and such, but since you are in your 3rd Tri, you are less likely than a 1st tri for your LO to develop a birth defect. Most of LO is completely formed by now, other than refining the central nervous system (as LO prepares to live outside womb), there isn't a lot of development. Primary 3rd tri is a period of growth and refinement of existing systems.
Bottom line - don't bring on unneeded stress. You got your flu shot, did what you could to stay healthy. Now just get some rest, drink lots of water and know that your LO is still growing away. Feel better soon!