WOW having had a PO302 error code (#2 cylinder misfire detected) on my 07 Nitro R/T 4.0 engine your issue scares me! I have seen head gasket issues and cam replacements as needed repairs to solve this type of codes. It looks like at least for now I corrected my PO302 error code with a simple additive. Chevron Techron Concentrate Plus Fuel System Cleaner - 20 oz.
Maybe in my case it was one dirty spark plug or injector? I'm sure if I drove the Nitro more it would not have been an issue.
My R/T is a very low mileage vehicle but lets face it, it is 12 years old and could use replacement of many of what you have done including spark plug wires. Don't know how long this low cost simple repair will keep working but it will go to the Dealer since I do have a backup "Lifetime Power train Warranty" if maintenance replacement items don't solve any future error codes. No way am I going to try to figure out myself and repair my Nitro when I might end up like you and some others just in case it could be a covered engine issue.
I have no suggestions except bad fuel or spark plug wires and hopefully you will find the cause and report back here so we can share the resolve. GOOD LUCK!
Nitro Year: 2007 (1 of 91,815 sold in 07)
Nitro Model: R/T 4X4 Stone White
CAT-BACK Exhaust, CAI, Projector Head Lamps
Fully-Equipped w/all factory options