The price seams ok for such an extensive build, a lot of mechanics under quote by accident it is just a fact of life. I should know cause our company also does it from time to time.
Maybe just go down and talk to him face to face calmly explaining that you are upset that you were told that your existing parts would support your requested power level. And would like to know if he could help you out with a retune if you source some other parts.
Just get a Nismo adj FPR and a new fuel pump and maybe source a second Z32 AFM and run a twin afm intake and just be happy with what power you get then, which I am sure will be enough to scare the living crap out of you anyways. These parts should come in under $1500.00.
Good luck mate.