I'm still not convinced it's not running out of fuel. Your car is acting a lot like mine did when my fuel pump was going out. Lots of power down low, stall out at the top of first (without knocking), then more power after the shift.
Does your car stall out at the top of second as well as first?
In my case, a new fuel pump solved the problem. Since you have done that already, I suspect a clogged/kinked supply line. The clog/kink might be allowing enough fuel by to let the engine run normally until the fuel demands are the greatest, high RPM and high boost. Then, you run out of fuel, the car falls off, it shifts, the RPMs come down, fuel demand lessens, and the engine starts to produce power again. When my fuel pump was failing, it would go crazy lean at the top of first, but only for a second right before it shifted. It never did knock, but I think that's because the fuel starvation was only for an instant right before the shift and the engine was able to deal with it without detonating/knocking. I wonder if you are experiencing the same thing?
Do you have any way to monitor the air/fuel ratio other than the stock O2 sensor? If you run out of other ideas, you might look into taking it to a shop with a dyno and a wideband air/fuel ratio device. If you can get the car to mess up on the dyno, it should be pretty easy to trouble shoot at that point.
There's a dyno where I work, and being able to watch air/fuel, timing, and just about anything else; all while in a controlled environment, while under WOT, with all the diagnostic tools near by is pretty much the ultimate in trouble shooting. The only hitch is when the car/engine won't duplicate the problems on the dyno. Hopefully, yours will mess up on the dyno and a competent trouble shooter (or you, if the shop will let you dink with the car while it's on their dyno) can find the problem.
Good luck, and let us know what it ends up being.