Welcome to the Forum.
My first question would be, Why did you change the coil? The OEM coil is about the best thing on the engine.
Did you use Performance Wires? Use dialectric grease? Anti seize on the plugs?
Looking at some of those codes, it looks like the coil could be the culprit
. Unless you mixed up the plug wires although it should run rough all of the time rather that after running for a while. How many miles? Did you pull the negative battery cable and let it sit for about 5 minutes to reset the codes? I have to assume that your PT is a 2.4 non-turbo (NA)?
I have more questions than you originally did, sorry, but some of this we need to know to help
__________________
2008 Silver Steel Metallic, Touring, NA, Sirius; Chromed door handles; lower grille; fog light surrounds; chrome front & rear bumpers strips; Airaid air filter; Bassani duals; Modesty Cover; Autolite AP5263 Platinum Plugs (.040); Crane Plug Wires; NAPA Ceramic pads; Blane hood struts; PTeazer Gas, Brake & Foot Rest Pedals, '05 Rear Step Pad, Stainless Door Sills, Llumar tint, "A" Piller chrome; APC Strut Bar