'98 to '04 3RZ swap ?

If I have 2 fully complete motors with all engine controls and mine is a 1998 3rz, the replacement might be a 2004 4runner 2.7 (assuming its a 3rz)
Does anyone know if I will be able to just swap out the valve covers and use the coil packs instead of the COP's ?
I assume the pointer for the pickup coil will be on all 3rz cams

if its a 4 port head, can I put my '98 throttle body and other engine control junk from my 8 port plenum onto a 4 port plenum ?
I assume my 5 spd bell housing will bolt up after removing the 2004 auto housing

 

You have to use the 2004 engine parts on the engine.

 

Changing from the 8 port to a 4 port will affect engine performance. You don't want to mix that. While the base engine is 2.7L, there are several mechanical and electronic changes that can cause problems with doing a swap over that many years.