yes you are right about the mechanical injector part and only a pump upgrade can increase the engine's performance. I will be removing my s-flow rear box soon. hopefully with some $$ i can get a replacement bullet for it cause a box would be costly cause frontier's piping is around 2.3-2.5" in size and its not a 2.0. the 2.0 piping size is the same as my old car the Daihatsu Charade(modded) and edward, you might had seen the car before, if not, ask Zam or Amir or any of the oldies which had seen and been in my old car before.
the regular exhaust shop i which i had visited and also the one that helped me through some of my exhaust mods on my old ride also did encourage me to maintain my original exhaust piping since i'm still running the stock turbo and also just recommended me to remove the front box and the rear s-flow box and replace it with a straight thru box and bullet. reason why i had not done that yet is because its bloody costly to do so. so maybe i'll just remove the rear s-flow box to improve flow for the engine but i'm gonna maintain the same piping size to prevent turbo lag and also too back pressure lost due to the straight flow setup.
btw, frontier turbo's only kicks in around 1.9k-2k RPM on the average. before that the engine is running purely NA and it can be really underpowered especially when climbing steep hills. i personally experiance this during my offroad trips where i had to engage 4L in order to make it up the hill without bogging the engine down in first gear on 4H. so with increase lag, offroading becomes slightly harder and when you are encountered with places where you would need to mantain low wheel spin and gain as much torque as you can to pull you out of the ruts and up hills, bigger piping is not an answer for that. =)
so yeah, thats my input on exhaust pipings for the frontier la. so most likely i would only remove the s-flow box and replace it with either a piping or a bullet. or if cawyn wants to do that first, by all means please try it out and lemme listen to the car i wanna know if its gonna increase the noise anot... hehe... relatively turbo makes less noise compared to NA as most of the exhaust note is muffled by the turbo. so im sure Phoenix would be quieter compared to Minizilla with the same setup. =)