Check engine light was on last week, found a hole in my intake runner, then replaced the intake runner. To turn of the CEL I disconnected the battery, and the CEL has not come on since

Sunday night and again last night when flooring the gas I discovered the hesitation.

Not sure whether this matters, but the new intake runner I purchased ( from dealer ) was slightly different than the original, I had to plug up a nipple that wasn't present on my original.

At normal operating speeds ( moderate acceleration, cruising below sixty mph ) the car runs fine