Yes.
I just ran across this recentlyas well. I was trying to use an '02 manufactured block on an '00 XJ which previosuly had a '99 manufactured block. I decided not to.
The engine mounts will not bolt on correctly. One boss on one side is short, the other side is long... Also about 5+ bosses will have to be drilled and tapped for the differences in accessory mounting. Also the XJ block you have probably has the oil sensor mount right above where the curved oil filter housing is cast into the block. The '02+ blocks do not have this provision for this mount nor is there a curve in the casting for where the oil filter mounts...
Not worth it I think unless the cost of fixing \ modifying the engine mounts and drilling + tapping the half a dozen or so holes is less than the cost of the engine. You will want to use a block from a 91+ but pre '02.... In 2002 I think they switched over to the accessories mounting differently.
George T.