Please take my advice to heart, since I have gone down the path you have already and then some. I have a gt3071r, built motor, additional mods, etc. With the gt3071r you must get an after market turbo manifold and custom weld a seat for an external wastegate to bolt up. The reason for this is the atp turbo will induce major boost creep and that may detonate your engine. You have to have full control over boost and with the stock atp internal wastegate, YOU WILL NOT. Next you need to get engine management. I recommend the cp-e standback which is a piggy back. Then I recommend the cp-e full control flash which will cure the throttle plate closing issue and if requested will take care of fuel cut as well. These options I just told you about are non negotiable. You have to have them if you are going down this road. Prices are as follows:
ATP GT3071R TURBO KIT: $2200+
CP-E STAND BACK: $600
CP-E FULL CONTROL FLASH: $500
PROTEGE GARAGE TURBO MANIFOLD: $500
TIAL 44MM EXTERNAL WASTEGATE: $350
CUSTOM WELDING: $80/HR