Well it was an ordeal but finally succeeded in making it work. I had searched these forums endlessly for help in finding the issue but never had any luck so Im posting my findings for any other poor sucker who gets involved in this swap.

Shot a rod bearing in my 252K mile 5.4 original motor and had to find a replacement fast and cheap. Located a craigslist ad for a local 2003 motor with 105K for $850 but it was gone when I arrived. The guy had a 2009 5.4 out of a van with 40k miles for $1000....said it would bolt up and I bought it.

He was right...it did bolt right up. Never swapped a motor in my life but necessity drove me into it. I was excited to finally fire it up and feel that relief that I was back on the road again....but what seemed at first to be vaccum leak led to a long drawn out search for cam sensor placement....checking part numbers between 2009 van motors and 2001 f150 motors and timing covers and cams and ring gears and cranks and on and on.

The 2009 van motor was NOT a three valve...my valve covers and intake fit right on it. It wasn't out of a truck...it was out of a van so there were no cam phasers on this motor either. The cam timing gear was the same part number (which is where I was thrown off from the get go). I tried everything and it wasn't the PCM had failed or the timing of the new motor was off or the cam sensor placement was off (even after drilling a hole in the head with some quicksteel epoxy and relocating the sensor....no help at all.

In the end...same part number or not...the cam gear in the 2009 5.4 van motor may be the same but in this case I took apart the top of the motor to see the timing marks were aligned just right....but the cam gear had eight recitifiers on it. Eight nodes sending eight pulses per rotation to my 2001 computer programmed to see one pulse per rotation.

I was hesitant to swap cams (at three in the morning) without more research about lift and duration between the two...and too driven to make this work and get on with my life so I got my dremel tool and cut off the seven extra nodes. I had lined up the cam mark positions to match my old motor to mark the correct and only necessary recitifer first...but yes I cut them mothers off and put her back together.

Walla! Magic! she runs better than ever. After a stint with a weak coil and such Ive successfully rid myself of the "Service Engine Soon" light that has been there for years.

So....long story short. If you're swapping an identical motor from a different year...and everything bolts up...don't forget to check that the cam and crank sensors will read to your computer properly. Check your cam timing and ring gears...which I completely failed to pay any attention to. If pulling valve covers on these was a piece of cake I woulda checked a long time back but since it was listed as the same part number I never did until there were no other options.

 

Reading this made me look in my Chiltons book. So you aligned your timing link with the node in line with the keyway of the camshaft sprocket? , then filed the others off?
I'm looking at the possibility of this very swap in the future. So if you had swapped the camshaft sprockets off the old engine to the new one, this would have been avoided, correct?

 

You should have the luxury as I did of having your old motor to use as an alignment tool. With the crank pulley mark set to TDC (cam lobes should make sense that you're not 180 degrees off), the drivers side cam gear alignment mark should be at eleven o clock and the correct rectifier node should be just at the leading edge of the cam sensor.

If you find like me that your cam timing gear has seven additional nodes...cut em off.

I didn't see how the gear could come off the 2001 camshaft...appeared to be pressed on.

Also...i would have had to remove the entire timing cover in order to get the chains relieved enough to swap cams or gears...it was monumentally easier to cut off the nodes.

Gotta take care not to damage the chain with a grinder. I used a small dre mel with a cut off wheel.

If I would been smart enough, I woulda taken of the timing cover and checked chains and timing and cam gears before putting the replacement motor in the truck.

 

I thought about u having to take the timing cover off later after I posted that. Thanks for the heads up about this. Good luck with your low mileage engine!
I don't blame you for not taking that cover off beforehand. Who would have thought it would have those other nodes on there anyway? Same part numbers, like you said. Glad you got it figured out.