i have a 2006 f150 3 valve 5.4 blown engine. I have a 2003 5.4 available, will it work?

The 2003 engine is the 2 valve version and will not meet the smog requirements for your 2006 truck.

But will the motor work without changing alot

Yes you can remove your 3 valve head assembly with cams etc, timing cover and intake manifold and bolt it all onto the 2v motor and it will work. Basically you have to turn the 2v motor into a 3v motor by swapping those parts.

All your pumps and pullies from the 3v motor need to go on that 2v as well. Its a bit of extra work but supposedly the 2v block has its benefits over the 3v block. Ive been looking into the same swap but they dont smog test here and even if they did im not sure it would teat much different as you would be making it a 3v motor but with a cast block instead of aluminum and the pistons are slightly different. This swap has been done many times, but usually in a 2v vehicle for the extra flow of the 3v heads and they use phaser lockouts with custom tune to work on a 2v pcm. With your swap you would be keeping the vct setup so its less work and money

If you want to use the complete 2 valve, it may work by using a 2005-2014 Econoline 5.4 2valve wiring harness and ecu. I don’t know if it would work or not.