I know the 4.0 engines have mirrored heads, can the valve covers be swapped between the two and will the bolt holes line up? I may have a clearance issue with a new alternator where the oil fill port may be in the way of the voltage regulator plug.

 

Assuming 1990-2000 4.0l OHV engine?

No, not really, the PCV Valve is on the other side, and the oil fill tube also has the fresh air vent hose
Both would need longer hoses if you swapped valve covers

I think they would fit but have to say I never tried it, and not sure how that would change clearance issue, if they are the same??