Factory rates them as 540cc, but you can see from
http://users.actrix.co.nz/richardm/Page ... tors_j.xls that they actually flow 560cc @ a rail pressure of 3.05kg/cm2 (~43.5psi) and can be made to flow 610cc @ 3.55kg/cm2(~50.6psi).
At a standard rail pressure of 43psi there's no way that a properly tuned 3S-GTE (which has a known BSFC of around .52lb/hp/hr) should be running at 100% duty cycle, unless it making around 430HP at the crank. Not that you can run 100% duty cycle anyway, given the injector dead time of 0.89ms you can only run around 95% above 6000rpm, even then you'll run into problems with injector flutter if you do it for any length of time. Given that you can't even get that sort of performance out of a T-78, there's no way you'll get it out of a modified CT26. So there must be something wrong in the tune if the duty cycle is that high.
Assuming you've checked fuel pressure and tuned with a WBO2 sensor, then the possibilites are that you have a bad injector, bad injector wiring, or even incorrect placement of the WBO2 sensor. If you haven't been monitoring fuel pressure then it could also be due to incorrect fuel pressure setting,a clogged fuel filter, bad fuel pump, or bad fuel pump wiring.
It's also possible that because the ECU you're using cannot do sequential injection and run the 4 coils at the same time, that fuel economy has suffered, which it will do. However I doubt that it's to the extent that you run out of injector capacity.
If you haven't used a WBO2 sensor and tuned by "ear" then chances are that you've tuned too rich.
FYI @ 85% duty cycle the stock injectors should be good for around 310whp at stock rail pressures and up to 340whp @ 50psi.