Well this morning, I didn't hear any abnormal noises when I started it up and put it in gear. I was hearing it every single morning for the last 3 weeks. It was like clockwork, start it up, put in in gear and knock, knock, knock...
Like I mentioned before, Toyota did not replace my exhaust manifold, they told me over the phone the noise was cause by my Fuel Pulsation Dampener. Of course on the paperwork they wrote that the cause of the noise was from the fuel pump, so ??
They also replaced my lower two cats per the TSB so perhaps I did have an exhaust leak at the flange where the manifold hooked up to the lower pipe, and this fixed it and the fuel related parts was just to get some cash out of me? Who knows, but the noise it gone for at least this morning.
Things to check before assuming its the manifold,
1. Exhaust flange bolts where the manifold connects to the lower pipes.
2. Fuel Pulsation Dampener (this little guys is very accessible, just relieve the pressure from the fuel line and swap this part out. I decided to pay Toyota to do it just in case it didn't fix the noise, I wouldn't get blamed for an incorrect installation. This part is located on the fuel rail on the driver side where the fuel inlet hose is. This bad dampener could cause fluctuations in the fuel line which could cause a cylinder to receive too much or too little fuel which in turn could create a knock.