The early Z3 had a completely different engine, probably the 1.9 litre.
My mom has a Z3 2.8 and it is a far more satisfying car and a better sporting convertible than the SLK. The SLK hardtop does give it a better 4-season ability, but a convertible should stored winters anyway.
The plastic rear window is a significant design flaw, but not a fatal one.
Any reason you're looking at these used vs. a new Mazdaspeed Miata or 2006 MX-5?