It would be a big wiring chalange with the later Mustang motor, all the electronics are now mounted up on the front passenger side, not what we are are used to seeing mounted on the fire wall. Greg used the OBD1 system from what I remember that made his wiring a lot simplier. Greg used the DOHC but think the best bet is as mentioned above is to go with the SOHC motor if you deside. I love my 3-v Mustang motor but being practical, I'd stick with a 302/351 based motor for the ease of it. Several suppliers now have even the 302 stoked/bored out to 372 cubes, that ought to get it done if you just want power.
Dave