Jeep Strokers

98 jeep grand cherokee pulled out the 4.0 and dropped a 4.6 stroker in used all 4.0 parts now having cps code put new cps in and still have codes my question is... Is there a difference between a 4.0 flywheel and the 4.2 flywheel automatic?

Absolutely, the 4.0 flywheel/flexplates have the "tone ring" for the CPS to see, none of the 258/4.2's were injected so they don't have tone rings.
You should have reinstalled the flex plate that was originally in the Jeep.

x2.
Reinstall the flexplate that was originally bolted onto the back of your 4.0 and that'll solve your problem.

I put the 4.0 flywheel back on I put a new cps and still getting loss of cps signal checked wires all look good new distributor can't figure it out

The tone ring on a flexplate is smaller circumference than the tone ring on a flywheel. Your crank sensor most likely isn't engaging at all. Don't ask how I know this.

When I pulled the old one out the end was eat up like it had hit the flywheel