I have a 2000 Z24 manual and I want to put the motor and trany into a 98 z24 auto with a blown motor that I picked up for free, the 98 is in perfect condition, the 2000 has seen better days (way better days).
I was told that there is a difference between the 2.4 motors between these years and that everything has to be changed, as in the computer, harness etc.
How much of this is true what do I need to put one drive trian into the other car

All true

Use the ECM and the wiring harness for the 2000 Z and keep your 2000 + transmission. (the Getrag 5 speed was redeveloped in 2000, and is better than the older trans)

One big difference is that in 2000, GM deleted the EGR Valve.... look to right of the intake manifold on the head.... the 98 Z will have the EGR, the 2000 will have a gaping hole with 2 screw holes... .

You'll need to cut the mounts out of the 2000 5 speed & weld them into your automatic car. After you cut off the automatic mounts too of course- fun fun fun !!! Turbo tech racing sells one of the mounts for the 5 speed. I think the other one can be ordered from GM. So, maybe you can get around some of the work.

Also, you'll need to swap the clutch pedal assembly over to the older car-.The automatic brake pedal is much larger than the manual one. I did a similar swap in my car so when I did mine I just took a dremel tool & cut the auto brake pedal down to the size of the manual swapped the cover over. Saves some hassle..

Also includes drilling a large hole in the firewall for the clutch. If you look at the firewall closely in the engine bay, you can see where the hole needs to be drilled. The line kinda goes up in this one spot.

You need to swap over the whole shifter assembly w/ cables. Wiring harness, computer, gauge cluster...

That should be it...

Is the wiring for the head lights part of the wiring for the ecm or is it separate harness.