Maf sensor/intake malfuntion

alright guys this might get a little lengthy but here's my problem. I have a 99 tahoe with a 5.7vortec. about 2 months ago i replaced the stock intake with an AEM BRUTE FORCE. everything went good up until the last two weeks. my check engine light has came on. i have had the computer hooked up to it and the malfunction is said to be the Mass Air Flow Sensor. I can notice something is wrong with it because at cruising speeds (55-70) it sometimes hesitates, not during acceleration or decel, just while cruising. Also at about this time my tahoe has started shifting a little hard from park to first and from first to second. It never does it going to reverse or to any other gears. (and wouldn't you know it, when i took it by the transmission place my baby acted as good as the day i got her.) I have been told that this has nothing to do with the maf sensor, but it seems wierd because it only does it when the service engine light has came on. Can all this be because of the added air flow into the engine? if so can a powerprogrammer fix the problem? or is my whole maf sensor shot? if so then what do you all suggest as a good replacement/upgrade? any hints, suggestions, or personal stories would help. Thanks guys....

and btw...the entire rest of my tahoe is stock.