Piston slap is usually a design issue, not an actual fault...I just threw that in as an example of other things that can cause a "knock" sound.
If the timing belt has slipped, the car would probably run very poorly, so that's most likely not your problem either...
If the other engine had perfect bearings and this one is doing the exact same thing, perhaps it's not an engine problem at all... something in the transaxle or torque converter could be wrong. I had an old Buick once that had a weird kind of "nuk-nuk-nuk" sound that was due to a cracked flex plate. I don't know much about the CD4E transaxle, so hopefully someone else will have some better answers for you.