Can I put a 2000 4.0 in a 2003 in place of the 4.6?

 

Yes. Direct swap no programming needed.

 

Depends if it's long block or short block. If one has SAI heads and the other doesn't, there will need to be some reconfiguration to get the ECU to stop complaining.

 

Tge 4.0 is a long block that I had the heads redone and gaskets.

 

Are the heads on both engines equipped with SAI?

 

Do you have a picture of sai heads?

 

they have those two little water tower looking things on each side of the engine.

https://www.roverlandparts.com/2ndair.aspx

if they both have them or both don’t, you’re good. If you’re changing from one to the other, you’ll need to reprogram the ECU and/or plug the openings if the new heads have them but the old doesn’t.

 

Those aren't part of the heads, so you may not know if they were there if you didn't have the engine in situ in the original vehicle.
With SAI, there will be two injector ports on each head, between the spark plug holes (beside two of the exhaust ports), as below:

The injectors look like this:

Most easily identified by the square faces under the threaded head.

 

I replaced by bad SAI 4.6 with a good 4.0, however, to get it to run right I also had to swap the ECU for the 4.0 ECU as well as the fuel pump. The 4.6 ECU was adding too much fuel to the 4.0 and causing it to misfire. The SAI fuel pump is different than the non SAI fuel pump, so change that as well.