The stock ECU is able to correct for air temperature, the PF, 034EIC, etc... doesn't.

Putting the injectors controlled by the ECU further from the cylinders could make the problem worse. It may have unpredictable results - the equilibrium between evaporation and condensation of fuel pooling on the intake tract will certainly be different than the ECU expects, it may be able to correct for this to some extent, or there may not be any noticeable difference at all. Experiment... see what works best for your setup.