The problem is that, while your 550cc injectors are ~20% bigger than what the ECU expects, the 2G MAS isn't 20% bigger than the 1G. It's "about" 20% in alot of places but it's not linear. That means that while the two effects may cancel to give you good AFRs in some regions, there will be other regions where your AFR is off. Also, these two effects end up putting your in the wrong load-row on the ECU which means that the timing is more aggressive than it should be. The point is, this was a common mod back in the pre-y2k era, but now there are better ways.
To do it RIGHT you need to have your chip adjusted to compensate for your injectors and your MAS. You'll have to do some research to determine whether this is possible on your ECU (I assume JDM ECU since you mentioned JDM in the original post). Contact Jeff (keydiver) Oberholtzer who runs DSMChips.com and inquire about a chip for your ECU / octane / etc.