I have run into this Problem tuning Supras for many years... Here is what I used tell those guys....
"Potential Problems caused by Aftermarket Intakes
MAF Sensor Housing Size
The MAF sensor only samples a small portion of the air coming into the system. From that sample measurement, the engine management system can calculate how much air is actually entering the system because it knows the inner diameter of the MAF sensor housing it is sampling from.
If the MAF sensor housing inner diameter changes in any way, the calculation performed by the engine management system will be incorrect. This means that the amount of air actually entering the system will be different from what the computer thinks is entering the system. This is critical because the computer determines how much fuel and timing to run based on this value of air. When it's wrong, it can cause the engine to run richer, or leaner, than it should.
With aftermarket intakes, it's extraordinarily common for the piping used to have a different inner diameter than the MAF sensor housing incorporated in the factory air box. This is due to the fact that the exact inner diameter of the factory MAF sensor housing is different than what's commonly available in the standard metal piping used for aftermarket intake systems."
That was for the Older generation of Supras (86-91) The Newer Generation had a MAP sensor... The Older ones used a Karman Vortex sensor that uses the same principals as a maf... We used to have to increase the Injector size from 440 to 550 and then tune it down from there. That all came about through alot of Trial and error... So I guess the Idea for the sonic would be Either get a Tune or get an intake system that is the same ID as the Stock unit and you should be fine... but I would put it on a dyno and install a wideband 02 sensor and make some pulls just to make sure.
I also wonder if putting on an afc neo would allow you to tweak that... It worked on Many Scion TC's I have done with a turbo kit installed. If I was still in that industry I would be working on a turbo kit for it as we speak... as I did with the TC.
Tim