Wow, alot to address here. Ok, first these are stock pistons. Never touched the bottom end during the rebuild. The piston slap was what I was considering. Would a piston slap give a similar sound? Keep in mind, the car was sitting for over 2 years without being run, do you think the noise would go away once warmed up? Or should the head come off still?
The guys working on the Supra now actually know what they are doing. I pulled it from the first guy, took it to a place called Precision R. Now I had another shop remove the motor because Precision R charged way too much. I look at the crank shaft, and the bearings, and there is no wear whatsoever. Precision R is asking me to have the crank tested at a machine shop to see if there is any cracks that cannot be seen by the eye, which can cause the double knock as well, even though there is no damage to the bearings. This sounds strange to me, but ok.
I do have confidence in these guys, its just that I am trying to figure out what is going on before we rip the whole thing apart, but it sounds like the head is going to have to come off.