I have a 2000 jeep grand cherokee 4.0 that has a misfire on the #2 Cylinder. It had a bad head gasket so i did the head gasket replacement and the 2nd cyl had a hole in it where i guess the PO had driven it with the bad head gasket and melted it. Bored out that cyl and put new piston in, got everything back together but it still has misfire in the same cyl. Has new spark plug, and new boot and of course the piston, what else could cause a mis?

 

The first thing to do would be a compression test, and if you find that cylinder low on compression, do a cylinder leak down test to find out where the leak is.