Again this is why I am not going to a bigger injector with a piggy back system.....
I still believe without going to a standalone ECU/TCU, the best way to do this is going to be 7th injector and O2 calibration. Like you said if you put bigger injectors in, even if you are using a piggy back to adjust the injector pulse width, while in closed loop the stock computer will continue to cut pulse width and timing until is sees the AFR it wants to see.
Example you swap in 415cc injectors they flow 31% more than stock. The computer uses its "canned" maps and at the regular pulse width you are running way rich at the O2 sensor, so it cuts injector pulse width and timing 30%, now your AFR is higher than you want, and your timing is way off the map, but you want to get lower AFR readings so you adjust with your piggyback, the computer cuts injector pulse width again, to stay at 14.7AFR, it is a loosing battle.
Now with the O2 sensor calibrated to read 14.7 when the engine is at say 12, then the stock computer wouldn't do anything to adjust fueling because it thinks it is happy, then you use a real AFR gauge to monitor and add any additional fueling you might need via 7th injector. Many 7th injector kits allow you to do a separate map just for that injector, so when you do stop running in closed loop and go open loop where the Toyota computer seems to want to run really rich, you also make sure you have proper fueling there. *This is basically what Safari did with their kit* someone please correct me if I am wrong.
It is far from a perfect, solution, the other solution is just to stay within the stock computer's A/F correction capability, but if you do push it a little and tune at say summer high altitude, when you drive down to sea level in the winter your truck wouldn't be able to keep up and would end up running lean, because the % of correction couldn't go high enough to fuel.
So in my mind I see 5 possible solutions based off of budget, power requirements?
1.) TRD Supercharger $3400 ~280hp
2.) Turbo, Stock fueling, and computer low boost, 275-300hp, very similar to the TRD Supercharger
3.) TRD Supercharger with custom A/W IC, A/W radiator and smaller pulley 320hp maxed out injectors
4.) Turbo, A/W IC, A/W radiator, Some type of piggyback system for ECU and fueling, stock TCU, 360-380hp pushed to max 400hp
5.) Full stand alone ECU and TCU, new injectors, new fuel pumps, built head, upgraded transmission, sky is the limit.
I am just talking out loud here, hope no one minds the rambling, but writing a post kind of helps me think options through.
That is also what I have found in many dyno tuning session. If you plan to run a stock ECU and adjust fuel with a piggy back of some kind make sure you do not go to big on the the injector. With a big injector and a piggy back system when you start taking fuel out (adjusting the MAF signal) it also effects timing usually advancing and that is about the last thing you want to be doing on a ECU mapped for a non turbo engine. It also has effects on Idle quality and transitional throttle points.
I have a friend that does lots of ECU work (standalone Motec, Haltech, Vipec, Bosch and others). When he was working and living in OZ he did quite a few cars where the Standalone was used to tune the fuel and timing. The stock ECU was retained for trans control and other things like idle. Said he should be able to do the same with my 1fz but would need to get the stock ECU plugs to make a jumper as well as Haltech Sprint 500 (or Sport 1000).