Don't hold your breath, the manifold cracks are from local expansion,
(Between the exhaust bolts)
A flex joint may help but I'm on the 6th complete exhaust (Only 1 header)
since I've owned my YJ (Bought new in 1994). It destroys cats, mufflers, hangers pipes, the 2.5
produces pretty harsh exhaust pulses and a stock one is not smooth at all.
My current one is lasting pretty good, its heavy aluminised tube,
welded steel muffler and a matrix/random tech cat. Its about 3 years old now, a new record for me.
The flex pipe probably would have helprd the issues I've had downstream from teh manifold though...
My Thorley header is like 7 years old and still in great shape.
Dave