Edit: also since the Cobra of 03 and 04 are DOHC the heads are different so the bolt pattern is probably not the same since the head gaskets will be different.
You can bolt 4V heads onto any GT block, it has been done many times in the past.
There is a difference between the 99/00 and 01 & up block.
The 99/00 were Windsor block, whereas the 01 & up were being made back in the Romeo plant. The reason the 99/00 were made in the Windsor plant was because of a fire in the Romeo plant. The block are slightly different.