The 05 2.4 block is not the same as the 02 and earlier design. Read up on the articles and threads on this as the blocks usable is outlined.

As far as megasquirt recognizing that crank trigger pattern, you are on your own as I am not sure if anyone here has used a late 2.4 block for the swap. The 2GNT head does not bolt up regardless, as the oil drain hole was changed as well. So unless you are planning on using the head that originally came with the block, you might as well toss it.