I replaced the Throttle Position Sensor and it seems to have fixed the issue. Inside of the TPS there is a plastic wheel which has two plastic teeth and those on the old one had been worn down by the metal throttle tab on the inside of the unit. I hope it fixed it for good.

In other news I replaced the EGR Valve, but don you all think I should just let the check engine light go off by itself or should I force clear it? If I force clear it I have to wait 300-400 miles for it to send codes again, and I need to get the VX inspected. Would the light go off by itself if the EGR problem is resolved?