The fact that you're using a ram intake means that you are forcing air into a system that is normally only exposed to vacuum pressure from the engine, this is probably what is causing the engine to run lean (too much air). A tune will tell the computer to compensate for this difference by adding more fuel than what it thinks it should.
this makes sense but since both cars are modded the exact same way, the problem should happen to both.
a couple possibilities are that there is bad O2 sensor or the maf sensor is not measuring correctly or there is a vacuum leak after the maf.
with the maf sensor not measuring right the computer sees the improper air (lower than what is actually coming in) and thinks that it needs to meter back the fuel causing a lean condition.
With the O2 sensor scenario, a bad O2 sensor can be pin pointed by watching live datastream. the front O2 sensor should be fluctuating and the rear one should remain relatively stable. the front one will fluctuate because it is a narrow band sensor and the computer keeps adding and subtracting fuel to maintain a 14.7 AFR. the second one should remain relatively stable becasue it is after the cat and monitoring what comes out of the cat.
and a vacuum leak can cause a lean condition because there is extra air being introduced into the intake stream that was not accounted for my the maf sensor thereby causing the afr to be lean becasue there is not enough fuel in the mixture.(extra air that the maf does not "see")
My best guess is there is a vacuum leak after the maf. if you can rule this out then id start watching the datastreams for the O2 sensors and the maf sensor. most likely a vacuum leak.
