The first few years of the 3.6's were the problem ones, but you would think most would have been repaired by now. I have a 3.8 JK but it only has 80,000 miles on it and only had to do a tuneup on it.
You could carry some tire plugs and a small air compressor for plugging a tire but shredding one i'll have to say that only happened to me 1 time in about 54 years.
My guess one set of wires are switched wrong, look to see which one is working right and look at the wires at the connector. Then look at the other connector to see if the colors match up the same.
If it only does it at highway speeds and not under that check the under hood insulation to see if it's getting sucked over the air filter intake and choking it out. It's happened to a couple other Members on here.