2000 GP With Very Bad Shuttering

Hey all. I have a 2000 GP with 3.1 engine. When the car is first cranked up, it runs perfect. As soon as it gets warmed up, it shutters between all shifts as long as you have the gas pedal pushed down at low speeds and low rpm. Give it more gas and the shutter stops. It's also started the shuttering while driving at speed between 55 and 65 mph. And it does it really bad while going up a hill unless you give it alot of gas. The exhaust seems to have a little bit of a " putter " effect when you put your hand in front of the exhaust pipe, sorta like a miss. I don't know what to do with it. Anyone have an idea that could help me? Also has new intake and head gaskets and held pressure fine on a test. thanks!

how many miles on this GP? and I would assume you did a tune up?

first things first i would check 2 most important things, fuel pressure and spark

Yes sir. Did a tune up and still no change. Checked the spark by pulling the wires off one at a time and had plenty of spark. The coil packs for the 2,5 and 3,6 cylinders arced off of the pack bolts pretty bad. 1,4 pack didn't do this. Also changed the fuel filter and still no change. The car has 163,000 miles on it. It started this after I had the harmonic balancer replaced. I know there's a sensor mounted somewhere around the balancer. I thought that could have something to do with it, but not sure.

your car has two crank position sensors. One is in the side of the engine block just above the oil pan rail, the other is behind the harmonic balancer. Normally a CKPS failure would cause no fire, not misfires. It sounds to me that you either have a bad coil pack or a bad ignition module.