4.0l heads are known for cracking between valve seats, it is a weakness in the casting.
My guess would be a running lean condition or EGR issue that causes a cylinder to run a little hotter, or a failed water pump or coolant leak which caused an overheating situation, anything that causes an over expansion in the head metal and the weak point shows up.
Just for future reference, if I have a running vehicle and plan on having to remove any exhaust parts, i.e. manifolds, cats, etc....
I take it to a local muffler shop tell them what I am doing and have them remove and reinstall/replace any exhaust bolts I will have to deal with.
Usual cost is $25-$50 so not too expensive
All they are doing is loosening and tightening bolts and nuts, to make sure they are not frozen, so it can be a pretty fast job.
And if there is a frozen one(almost always, lol) they have all the tricks and tools to get these stubborn nuts and bolts loose, they do it every day, so are fast and have replacement nuts and bolts in stock.
I did have one broken manifold bolt once, I told them not to replace it since I was pulling the head and could do it myself.