My problem ended up being the CKP/ Crank Position Sensor. It was a little cracked and wires were a little tweaked. The part was about $45 at Pep Boys. You need to remove the passenger inner plastic fender to gain access to the sensor. CKP is mounted between engine block and trans. behind the trans. dipstick tube. There are two bolts with allen heads. Three wire connection: Red, Green, Black.
NOTE: When my nephew replaced his trans it ran rough right after also. His just needed a fresh battery and then ran fine.