2.5L Misfire

Trying to help out my young niece. The car (2000 Dodge Stratus w/2.5L V-6 automatic) was purchased approx. 2 weeks ago from a small dealer. Past couple of days she started experience an issue with the driveability, took the car back to the dealer, he scanned it and told her it was a #2 cylinder misfire and he be happy to have his mechanic fix it, but it would not be covered under the thirty day warranty because it was electrical.

So I go check out the car to see what the symptoms are. It has a stuttering hesitation under accelleration that really seems get worse hotter the car gets. It happens whether you're leaving a stop light or acellerating on the highway. I bring the car to my mechanic friend who scans it with two different computers and both come up with a cylinder 2 misfire, but also a random multiple misfire. We also "smoked" the engine, but didn't find any leaks, and also tested the EGR valve just to rule it out, and it seems to be OK. He couldn't nail down anything specific. We checked the spark plugs, which are new Autolite double platinum, and the wires appeared to be new as well. However, the cap didn't look like it had been changed in a while so I changed the cap and rotor. This brought little to no improvement.

So I turn to you guys. Anyone have any input on this?

Do not run autolite plugs in a dodge.Use champian plugs.Allso check compression.U might have a bent valve in the head.And check if you are gitting spark from the #2 wire.

i would take #2 out and see what plug looks like they may have cracked it putting it in. also take a old plug or same one see if spark is yellow or blue yellow is not good. have you had coil checked?

I will try your suggestions and post my findings.

I would use a ohm meter and check the plug wire it should read around 1/2 scale. I've found a lot of cheap wires aren't crimped properly. Use a stethoscope and make sure the injector is working.
http://www.autopart.com/tools/toolsmain/tool/T_2015.htm
This is a picture of one. Also do a compression test as this will tell you many problems. Haynes will tell you how to ohm a coil. Normally unplugged put 12 volt on the positive and you should get 12 volt on the negative.