1. The 100,000 - 125,000 number is roughly the average for Iraq alone. 200,000 overall is still lowballing it compared to earlier studies even just in Iraq.
2. There are still studies that put the numbers over 600,000 for Iraq alone.
3. See above.
You can't really wage war on a non-governmental entity. They have no borders, no set-in-stone infrastructure. They can move from country to country and avoid death or capture.
By the way, al Qaeda has succeeded in its goal of terrorism beyond its wildest dreams. Due to their actions, those in power have an excuse to erode and infringe upon our rights as they have been since 2001. This is exactly what they want, to bring down the American way of life by way of fear as revenge for our earlier meddlings in Middle-Eastern affairs.
Considering that at this rate the Constitution will be entirely meaningless in a decade or two, they have achieved their objective. We, on the other hand, are digging ourselves into several very deep holes at the same time and have achieved nothing decisive other than a massive waste of taxpayer dollars, trampling of our own Constitutional rights, and general ****ery by the government to give themselves more power.