When you make that many changes at one time, things like this are bound to happen. Let's start with the obvious, knock those out first (no pun intended), and then see where you are at:
1. You did hot-wire the fuel pump, didn't you? If not, buy a hot-wire kit and install it. It has been repeatedly documented that the stock fuel pump wiring won't supply enough voltage for a high-volume pump.
2. Adjust your TPS per the instructions in the link that SS502 provided above. With the car RUNNING at idle, the TPS volts should be no higher than 0.44 volts. I always set mine to 0.42 to 0.44 volts with the car running at idle, and it works well. Understand that 0.45 volts is the cut-off between "engine idling" and "pushing on the gas pedal" according to the ECU.
3. After you get the TPS set, shut the car off, then turn the ignition back on (but don't start the car). Push the gas pedal to the floor. Make sure your TPS reading goes to a value over 4.25 volts (preferably higher). If not, reset your TPS again, but this time slide the entire sensor rearward as far as it will go, get it to 0.42-0.44 volts at idle with engine running, and re-verify the gas-pedal-floored reading with the engine off.
4. Start the car and get it warmed-up. Remove the vacuum line from the fuel pressure regulator and hold your thumb over it. Adjust the fuel pressure regulator to show 43 psi with a known good fuel pressure gage. Reattach the vacuum line.
5. Now, go for a short drive that has lots of different speeds and loads. City driving with stop signs, etc. is the best. This purpose of this is to give the engine computer (ECU) the opportunithy to learn the new TPS and fuel pressures at a variety of engine speeds and loads. As you're driving, watch the BL screen on the scan master. After driving for a while, you should see the BL's adjusting, and after they settle, they should all be close to 128 (I would say 128 plus-or-minus 10 or so). If you see that, you should be in pretty good shape. If not, you may need to richen (if BL's are all on the low side) or lean (if the BL's are all on the high side) by using the chip controls.
6. Once all of this is done, and you are sure they are all good, adjust your wastegate actuator rod to get 16 psi of boost on your boost gage (you do have a good boost gage in your car, don't you? If not, GET ONE). Start with the rod on the LONG side, just barely tight over the wastegate puck, and then shorten it a little at a time, doing a WOT run after each adjustment. Even with 91-octane, you should be able to get about 16 psi with no knock, if everything else is OK. If you get to 16 psi and have no knock, try 17. If you can run 17 psi with no knock, try 18 psi. I'm guessing that somewhere around 17 to 18 psi, you are going to see knock, because 91-octane just can't support that much boost. Once you see some knock, back off the actuator rod to about 1 psi lower than when you saw knock. I suspect you will end up around 16 to 17 psi. If you do the above, you should have a safe tune. As a final verification, watch your O2 sensor reading during your last WOT run. It should be no lower than about 790, and no higher than about 860. If you're somewhere in that range, you should be OK.
Good luck, and let us know how things go...
