bad skip @ low rpm/speeds

so im looking for alittle help/advice here. im a toyota guy myself, so im not to familiar with mazdas, but i can find my way around with alittle direction! my girlfriend has a P5, its an '03 auto tiptronic and it definately has some slip in the tranny, especially first. also it has a bad stutter/skip @ low rpm and speeds, as well as putting the throttle to the floor @ higher speeds. ive checked out everything, plugs, wires, coils, maf, tps. in drive, with your foot on the brake, every few seconds it has a small skip. very easily noticeable due to the k&n intake system. i am getting a check engine flashing light, this is why i have been checking out the motor. i know some of my skip/stutter may be due to the tranny issues, but i dont think all. haven't taken it to get diagnosed yet, guess i outta. any ideas? TIA!
 
Have a mech drive it and see what he things...it sounds like a torque converter to me, but I don't know a whole lot about auto trannys...my previous car was an auto and the symptoms sound the same. In my case it was the torque converter, so I would guess that could be it.
 
get a new fuel filter. its no more than 30 dollars. its in the tank itself which is very easy and accessible through the inside of the car. under the back seat. there is "how to" on this forum. my car would skip when my car was under 2k rpms and i would give it full throttle. this fixed it immediately. dont know bout the transmission problem though. btw my car had about 118,xxx miles on it when this started happening.
 

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