Have a 00 ranger and computer set up for flex fuel.
installed a 2002 motor, trans and wiring harness. Worked for a while but a little rough. Grew worst with roughness, sluggish and ideal rough. Throwing a maf code. The maf sensor I am using has 4 prongs and the 2002 connector/harness has 6 wires. Could that be my problem (running a 4 pin maf on a 6 pin set up)?
I did change the fuel injectors to flex fuel.

 

Yes, if computer needs 6 wire MAF then that's what you need to run, the extra 2 wires are for the AIR TEMP sensor, in earlier years Air Temp sensor was separate, on the intake or air cleaner box
CEL(check engine light) should be on with an Air Temp sensor "circuit" code

How did you manage to plug in the 4 wire MAF using the 6 wire plug in?
The 2 outside wires(1 and 6) on the 6 wire plug in were for the air temp sensor