Only two out of four cylinders are firing

Start by checking the diagnostic fault codes. Do you have a single or dual camshaft engine?

Be aware that each ignition coil fires two spark plugs at the same time, and anything that breaks that circuit will cause both plugs to have a loss of spark. That includes a single bad spark plug wire.

I have a Chrysler DRB3 scanner for my vehicles. Most aftermarket scanners have a test mode similar to Chrysler's "ATM", (automatic test mode), that allows you to command the engine computer to fire the ignition coils without the engine running. See if you have that capability, then check for spark on all four cylinders. If you do, that proves the ignition coils, engine computer, and all the wiring are okay. At that point I would be suspecting a problem with the crankshaft position sensor.

The reason I asked about the number of camshafts is there has been a common problem that causes a loss of spark from one ignition coil, but as far as I know, it only applies to the single-cam engine. The fault code would be "cam and crank sync".

Under your "inputs and outputs" screen, look for the crankshaft position sensor and camshaft position sensor, and see if they are listed with an indication as to whether their signals are showing up during cranking. Mine lists them with a "no" or "present". If either sensor is shown as sending no signal, or it is intermittent, that is the circuit to diagnose. Those sensors often do not set a diagnostic fault code simply from cranking the engine. They set when a stalled engine is coasting to a stop. If the battery was disconnected, that would erase those codes, then they may not set again. That is why the live data screen on your scanner is the best thing to have.

Also, consider that the engine computer will shut the engine down if the timing belt jumps two teeth, to protect the valves. At one tooth off, it is supposed to turn on the "check engine light". At three teeth off, valves could be hit and bent by the pistons. Two teeth off is real close to still running, and it can be right on the borderline where the computer cannot decide if it should stop firing injectors and ignition coils. The symptom often is a failure to fire just one coil.

That adds an important new dimension to the story. The two engines are obviously different since the sensors are different. That means the Engine Computers will be different, but the wiring harnesses will be too. The concern now is the notches on the tone wheel on the crankshaft. When the sensor ring is on the flywheel, they were different from one year to the next. For the V-8 engines, there were four series of notches. Some groups had four notches for every group. Some had four notches for three of the groups, and five notches for one group. When the computer saw the five pulses, it knew which piston was coming up on top dead center. You may have the same thing. The fault code indicates one or more pulses from the crankshaft position sensor is not showing up at the right time relative to the pulses from the camshaft position sensor. That could explain why the computer is firing only one ignition coil but not the other one.

The way to know for sure is to look up the part numbers for the crankshafts for both engines. In this case there are a lot of different choices. I don't know what the differences are. A timing belt that is jumped one tooth will set code 340, but usually the engine will still run. The computer shuts the engine down at two teeth off to protect the valves. If you haven't checked the timing belt yet, do that first. If that is okay, look into the compatibility of the two engines.

The only thing you have to do is be sure the timing belt didn't jump a tooth. After that, the Engine Computer sets the synchronization of the two sensor signals electronically and puts it in memory. That makes up for slight manufacturing tolerances. The Chrysler DRB3 scanner has a selection that performs the sync relearn too, but I've never had to use that. When I've replaced parts, I just cranked the engine, and it started. At that point the relearn had been done automatically.

The next thing you might consider is visiting the people at the dealer's parts department. They should be able to tell you if the two crankshafts are interchangeable.