[Three_Fingers]

Sounds like the comp is already trying to compensate. Trouble is-you screwed up the fuel aspect of the equation.
You need to keep as close to a 14.7:1 fuel/air mixture to get the maximum outut and an efficient burn.
If you change one of those proportions-you gotta change all the others, too.
You put bigger fuel holes in it-the computer which is still thinking stock says "WRONG!" and tries like hell to lean out the mixture it knows is wrong.
Blame your O2 sensor for this and your ECM's internal fuel map data.
The O2 sensor reports to the ECM that the mixture is too rich now-the O2 sensor is a stupid bird really-it's just an averaging device. Which means that the ECM will take that O2 info and compensate for the richest/leanest injector and shove things hard the OTHER way to try to compensate.
Al the ECM knows is what it's programmed to to keep a stock motor running.
X amount of time opening an X sized fuel aperture =X amount of fuel delivery to keep running efficiently. (This is called injector driver pulse width-the amount of time the computer holds a certain sized injector open)-the computer is programmed with values for this under stock conditions.
You make that fuel hole bigger and you've just gone beyond what the comp is programmed to compensate for.

You can add the bigger injectors-if you have the proper and proportionate air intake/exhaust size increase as well,(try breathing thru a soda straw underwater and you'll see what I mean-if the motor can't breathe right-it won't run right..) and then you have to reflash the PROM with new fuel data for all the conditions it will encounter with the bigger fuel/air holes.
Then there is the reprogramming of the cold start maps. ("Open loop data")
The O2 sensor doesn't generate any voltage until it reaches 600 degrees F, so the ECM ignores it and goes by coolant temp sensor and IAT sensor data until then or until about 2 minutes have passed, so meanwhile it refers to a pre-programmed pulse width map that is supposed to support efficient combustion until the O2 sensor comes online-sending the ECM into "closed loop" mode where it controls every aspect of the engine's operation.

"Power chips" will accomplish this-but you gotta know the numbers you are looking at-ECMs talk in hexadecimal.
Each hex value stands for a pulse width under a given condition-the conditions change rapidly and everything in between has to be accounted for to fill in the spots between conditions. Other hex values speak of ignition timing, possible sensor data combinations, crank position, cam position, throttle position, knock sensor data, IAC valve position, vehicle speed/load data, gear position, RPM-it's a lotta damned stuff that ECM has to think about-nevermind the values that are programmed in there for when it has to guess.
You're talking more numbers than you can look at in one day.
Usually performance setups come as a matched set.
The injector size is based on the chip's fuel data maps-the air intake is matched to the anticipated fuel delivery and the engine's displacement, cam overlap, ignition timing, etc.
In the old days it was more guess work, but carbs made it easier because all you had to do was turn some screws and listen. We got some serious power out of those old setups, but they were still horribly inefficient. Fuel injection is exact. Change one value without changing the others in direct proportion screws things up.
Ya just can't guess anymore.
That's why serious tuners have all that computer equipment and software to monitor and change stuff around-it's necessary.