Is the current ECU tunable?
If it is, that would be the best way to go about it.. put it on a dyno, with AFR meter, do a few base runs, and go from there.. maybe it needs more fuel higher in the rpms at WOT (that is my feeling according to the description).
A custom map on a dyno.
The mods you did should make it breath better at higher rpm's ... The ecu will not be able to compensate if the extra air goes in mostly in WOT.
You might be able to go around that by playing with different size injectors or fuel pressure,.. at the same time ..the ECU might compensate for the bigger injectors taking you back to the beginning.
No real way of telling if you don't have an AFR gauge.
This is what i think is happening: (only that you are not actually getting the extra fuel required at those high RPM's)
The same that same graph could be used for the AFR as well:
It is probably lean for high rpm/load/ WOT but might still be to low to actually trigger a lean condition error...or the ECU might just ignore it since it's in open loop anyway.