I swapped my 2000 Ford flex fuel motor with a non flex fuel motor... Everything went ok.. I changed everything besides the fuel rail and lower intake manifold... I'm getting lean codes on bank one and 2.. any help would be great.. and it starts ok but idles rough for a few minutes and acts like it's either misfiring or starving for fuel

 

The Flex fuel engine used bigger injectors so it could run ethanol, which requires a higher flow of fuel

You will need to swap those in.

The flex fuel computer is programmed with the Size of the injectors, so it "knows" XXX amount of fuel will flow into the engine if it opens fuel injector for 100ms(milliseconds)
If you put in smaller injectors(from gas only engine) then computers calculations will be wrong, only XX fuel is flowing into intake when smaller injector is open for 100ms

So computer has to open the smaller injectors longer, 130ms, that means it's calculations are 30% LEAN, thats what a lean code means, it doesn't mean engine is actually running Lean

So put the correct injectors in or swap in a gas only computer

I think the 2000 3.0l Flex used 21lbs injectors, and the gas only 14lbs
Later years with 3.0l use 24lbs for flex

The LBS is pounds of fuel per hour if injectors are left open
So flex injector can flow 21 pounds an hour
Gas only 14 pounds and hour

They use Pounds because air:fuel ratios are Pounds
Gasoline needs 14.7 pounds of air to 1 pound of gasoline, 14.7:1 ratio
Ethanol is 9 pounds of air to 1 pound of ethanol, 9:1 ratio

Since a 3.0 LITER engine pulls in air at the same rate, lower ratio requires MORE fuel to be added to that air at the same RPM

 

Did you find what the problem was with the flex fuel swap?