I would recommend just swapping the block and heads, then you can use your intake, fuel system and all sensors and controls, no new wiring needed.
1991-2007 block and heads will work.
You will need to change the oil pan and oil pickup if new 3.0l is from a 4x2
'94-'01 had roller tappets
You can also use a 3.0l from a Taurus or Sable, but you DO need to change the head gasket to Ranger style for coolant flow.
Flex fuel was computer, fuel sensor and fuel injector related so won't be effected by different block or heads.
The head dome design was slightly different for flex fuel but people have changed flex fuel heads to older 3.0l heads and they still worked fine for gas or ethanol.