I believe the problem has been solved. Checked all the vacuum hoses around the fuel injection system and there was a small leak due to a split in the rubber on the air breather vacuum hose that connects from the valve cover to the bottom of the air cleaner (The split was on the end that goes into the valve cover).
Replaced the hose and the car seems to run better. No longer hesitates upon accelaration.
Since the hesitation wouldn't occur until after driving for a little while, my theory is that the cracked hose would slowly loose its vacuum capablities and cause the low idle/hesitation problems.
Thanks everyone for your help!