Use the multiport alternative, Brian.
Give a good look at the MS3Pro Plug and Play system that DIY autotune has for the 03/04 Mach 1's. It uses an OEM harness with OEM sensors and is programmable for any engine size you might want to use. Great engine protection, traction control, knock detection and prevention s/w that uses OEM Ford sensors. Get an engine harness out of a salvage yard and you are good to go. Here is a link =>
MS3Pro PnP and here is an install video, click here =>
Install Vid. they ship it with a tune ready to go. When you change engine displacement the ECU scales the tune for the change in displacement. DOHC or pushrods make no difference unless you go for a TiVCT deal like a Coyote an then you just disable the variable cam timing with a mouse click.
ECU comes with a tune ready to go, OEM Ford sensor expectations, tuning software and data logging software.
Ed