The only thing that would happen from low fluid is the bearings inside the center section going bad from low/no oil. Filling it up to the proper level wouldn't have saved any bad bearings.
To get a stubborn air pocket out that can get trapped in when draining the coolant and add new. It will usually cause a overheating of the engine with trapped air in it.
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.