Egr is definitely different. Just get a block off plate and a cap for the manifold and delete it.
Like previously stated it may be easier to swap the heads and what have you. You'll see bigger gains keeping the npi pistons as well.

 

The older OE 5.4 is spent, low compression, power, black oil etc...must be replaced. I did a good amount of Googling and several people are said to have done the swap using the 98' computer and putting all the electrical stuff from the 98' on the 03' so the OE wiring will work. It is said to work fine but an additional tune could help. I bought an excellent condition used 03' 5.4L with great compression. I'll take the extra 30 hp the PI will add. This is just my daily work horse for woods, hunting, towing and street. I have some SS shorty headers to install in-place of the OE rusted cast iron ones. I plan to first install new seals and gaskets on as much of the 03' (including new Felpro valve guide seals) before installing since it has just over 100k. Need help with fitment of EGR air tube, I think the 03 is the one to use because the plastic intake probably puts the EGR valve in a different location. Some of the replacement ERG tubes have an accordion section that gives some measure of leeway on fitment, but needs to fit in the stock exhaust man. position. Local dealer today said they have one for $85.00 plus tax. Rock auto has a Standard brand for $50.00 with what looks like a SS tube like the OE. I've heard bad things about the Dorman parts coming from China.

 

As I stated above I was told the OE harness and CPU will work fine, just add a tune. My purchase was based on that info. Don't suppose my Edge Evol setting 3 will help? My OE 5.4L has the COP's on each cylinder, just replace another one a while back. I'm pretty sure I'll be needing new cats too. I can get Flowmasters cat with y-pipe OE fit for around $600.00 for both sections from RA. I'm not looking for a race car here, just a nice boost in hp from what I previously had with the 98' npi and another dependable 100k or more out of the truck.

 

Planning to keep the OE CPU and make it work. I've heard it will and run just fine but with an added tune I could realize the full potential the Ford engineers intended for the 03' PI in my 98'.

 

I'm not going to replace the whole wiring harness and pcm. 9 years ago I had to buy a new OE pcm as mine failed costing me plenty at the dealer.

 

So the older injectors will work with newer 03' plastic intake?

The COP's I'm using are the MC DG-508's.

So new o-ring on the water outlet tube will do the trick. Where doe that go, to the heater core?

 

Money and time already spent. Must go with what I've been told will work fine and have got to swap it soon. After all, the MAF senor doesn't know what block is in there. It will add a bit more fuel to the trims to get an efficient A/f ratio right? The o2 sensors will feed back and correct mixture as needed. So I've been told by a guy that says his works fine Out of touch with him now though darn-it, that's why I'm here now.

 

Accept I don't exactly have the "Power nation" at my disposal to hand me all these free parts. Just want a very dependable daily driver with the added 30 hp the 03' PI offers.

 

Won't blocking off the ERG mess with the computer in some way?

 

Yep it'd have to be dealt with in a tune.