Is timing computer controlled? Is it ok to pull spark plug wile running to test for bad plug/wire?

Yup, it's computer-controlled and not adjustable. Rather than pulling wires off, it's better to poke a grounded pick through the spark plug boot and short the spark to ground. You'll have NO voltage rather than very high voltage that may insist on finding another path to ground. That can lead to arcing and carbon-tracking in the distributor cap. By "poking", I don't mean poke a hole in the boot. I mean slide the pick between the wire and the boot.

Mixing up two or more wires is the most likely cause of the misfire. The second most likely cause is pulling a terminal off the carbon-impregnated thread in the wire. You can pull the metal terminal out to fix that but they will usually start arcing soon. Since you installed new wires, that's not a concern.

Not sure what you're referring to. There's nothing to reset. What WILL happen if you disconnect the battery is the Engine Computer will have to start rebuilding its stored data that it learns over time related to short and long-term fuel trims. You will never know that's taking place. What you might notice is the engine won't start or it will stall at stop signs unless you hold the gas pedal down 1/8". The computer has to relearn "minimum throttle" before it will know when it must be in control of idle speed. You also won't get the nice idle flare-up to 1500 rpm when you start the engine. To relearn minimum throttle, drive at highway speed with the engine warmed up, then coast for at least seven seconds without touching the brake or gas pedals.

I can share how the ignition timing works too. Spark timing is based on the crankshaft position sensor's pulses. To advance the timing at higher speeds, the computer can't wait for a set of pulses, then fire a spark plug sooner. Instead, they have a certain amount of delay built in. As an example, the pulses might arrive at 30 degrees before top dead center, then the computer calculates a 20 degree delay based on engine speed, THEN fires a plug. That means the plug really fires 10 degrees before TDC. To advance the timing, the computer just waits less time between the crank sensor's pulses and when it fires the plug. The crank sensor's position is fixed and can't be adjusted.

With the old mechanical distributors, ignition timing could be advanced for increased engine speed and for decreased engine load. With today's engine controls, timing can be advanced electronically for a whole pile of variables including coolant temperature, intake air temperature, whether spark knock is detected, and things like that. The goal of these systems is to eliminate the minute timing variations that could lead to increased tail pipe emissions. Worn distributor bushings that let the shaft wobble, and sloppy timing chains that made the camshaft timing fluctuate were the two main variables that were eliminated.

The only function distributors have now is to route the spark to the proper spark plug. Many of them also have a camshaft position sensor inside but on Chrysler product it's pulses are used to synchronize injector timing. You'll never feel any change when turning the distributor. The fuel sprays from an injector right next to the intake valve, then waits for that valve to open. If you adjust the distributor to make the injectors pulse sooner, that just means the fuel has to sit around a little longer before the valve opens.

No, you still have to have the wires routed properly. All the Engine Computer knows is it's firing the ignition coil. It has no idea which plug the high voltage is going to. As the distributor shaft turns, the rotor sends the voltage to the next plug in the firing order.

If you have the 4.0L inline 6 cylinder engine, the firing order is 1, 5, 3, 6, 2, 4. The terminals on the cap for cylinders 2 and 4 are toward the front with number 4 being next to the hold-down screw. The cylinders are numbered from 1 in the front to 6 in the rear.

If you have the V-8 5.2L (318 c.I.), The firing order is 1, 8, 4, 3, 6, 5, 7, 2. The cap terminal for cylinder 2 is toward the front. Next to it is the terminal for cylinder 1 which is next to the hold-down screw. The cylinder numbering on the engine is driver's side, 1, 3, 5, 7 from front to rear, and passenger side 2, 4, 6, 8, also front to rear.

Both distributor shafts turn clockwise. To add a little confusion, note that on the 5.2L, cylinders 5 and 7 are next to each other in the firing order and they're next to each other physically on the driver's side. When you clip the wires into the holder bracket on the valve cover, it's common for do-it-yourselfers to clip the wires in numerical order to make them look neat and pretty. That puts wires 5 and 7 side-by-side. The current flowing through one spark plug wire sets up a magnetic field around it which can "induce" a voltage into adjacent wires. That means it's possible for the spark to cylinder number 5 to electromagnetically cause a spark to occur at plug number 7 as it's on its way up on the compression stroke. This is much more of a problem on high performance engines with high output ignition systems and is a well-known cause of blown racing engines. That induced spark ignites the fuel WAY early in cylinder 7 and tries to make that piston go backwards. It is customary for mechanics to move the number 5 wire to the front of the wire holder and to move numbers 1 and 3 back a spot. It doesn't look quite as pretty but it keeps those two wires further apart just as a precaution.

Happens to all of us sooner or later. Happy to hear it's solved.