You're partially right. There is more heat and velocity next to the engine but that's not what spins the turbo. it's matter, and matter is not reduced farther back in the exhaust system. the exhaust velocity slows down due to cooling, but the cooler exhaust is more dense and therefore spins the turbo up just as well. It's actually a little bit better farther back because all that heat boils the oil inside the turbo housing on a typical turbo setup.
you're always going to have backpressure when you squeeze all that exhaust through an opening the size of a penny, but that is not necessarilly causing these engine problems. running lean due to using a supplemental injector would be my guess.
if you upgrade to larger injectors, I don't think you will have any problems. also, the passenger side fuel rail is fed by a tiny rubber fuel line that connects to the driver's side fuel rail. I would recommend ditching that and getting something a little beefier to get fuel to the passenger side fuel rail.
good luck!
p.s. I just ordered me a new turbo today