Excuse my lack of knowledge when it comes to this...

There's a long back story so I will try to keep as short as possible. I had cracked exhaust manifolds - changed them out for some stainless headers. Huge PITA. Started melting wires, got all kinds of misfires. I finally thought I got everything figured out with high temp wires and boots and rerouting them a bit. This lasted a couple of months but two days ago when leaving work I got cylinder 6 misfire.

Now I don't know if this is coincidence or not but I changed the tune on my hyper tech back to regular octane from premium the day before I got the misfire this last time.

Said screw it. Ordered replacement exhaust manifolds that night. Got them installed tonight, replaced the plugs while I had everything semi easily accessible because I'm at ~92k. They were pretty worn and nasty looking about a .065 gap.

Got everything back together and fire her up and its misfiring worse than before. I'm getting code P0300 so multiple cylinders now. I've checked the wires, they seem fine. Is it possible that the ignition coil is no good or what am I over looking?

 

I assume since you are talking about 92K miles this is a 3.8.

First of all, it's highly unlikely the exhaust manifolds had anything at all to do with your misfire.

Secondly, the cause and effect here is that you disconnected a bunch of stuff to replace the manifolds, and when you reconnected everything, now you get a P0300. P0300 can be very hard to chase down. But some things you should know, especially at 90K:

P0306 can be caused by many things. Every time someone hears "misfire" they immediately think "ignition" but it's not the only cause. At this mileage I'd say a bad ring, cracked head, or bad fuel injector is just as likely or more.

Step one when you get P030x anything is to replace the coil pack, plugs, and all of the plug wires.

Once you do that, if you still get P030x ... if it's a P030x and x is a number from 1-6, then do a compression test to verify you don't have a low cylinder, and if that checks out, swap the errant fuel injector with the one next to it and see if the problem follows the injector ... so for example if you have P0306, swap the #6 injector with another one like #5, clear the codes, then run it and if you get P0305 you know you have a bad injector.

P0300 is a far different animal. If you have that code the first thing to check is whatever triggers the ignition and fuel injector pulse. I don't know what this is exactly on a Jeep 3.8 or how it works but it will be some combination of a crankshaft position sensor and camshaft angle sensor.

But in your case, since you unhooked everything, I would say you probably either didn't get something connected all the way or you broke something (wire, etc.) inadvertently when you were making your exhaust manifold change. So you need to pull all of the ignition parts back off, chase every wire to make sure you didn't crack one or crack a connector somewhere, then reinstall, preferably with a new coil, new wires, and you already put new plugs. Verify you have all of the plugs tight while the wires are off. Go over your work with a fine toothed comb. It's not a coincidence that a) you did some work and then b) it misfires. The work you did is almost guaranteed to be the cause of the P0300.

If you're lucky then you will get everything back together and working to the point where you don't have a P0300 and you're left with the P0306 you started with, which is probably a bad injector, poor valve lash (valve not closing all the way), worn rings on #6, burnt valve, or a cracked head. In that order. Bad rings, burnt valve, valve lash, and cracked head can all be checked with a compression test, but to know which one it is will require adjusting valve lash first, then if that doesn't fix it, you have to pull the head.

Good luck

 

Had a cylinder 2 misfire this past week and changed plugs and wires (plugs were god awful). Start it up and was handling worse with multiple misfirea. Turns out I had wire 1 and 3 swapped. Forgot it went 2,4,6 then 1,3,5 at plugs then on the other end 2,4,6 them 5,1,3