Ben, normally you would replace the rotor then reinstall the brake caliper without the new brake pads in place. Then depress the caliper pistons and install the new brake pads. I own two 1995 E320's and never had any problem installing new brake pads after replacing the front rotors. Having said that, I purchase new rotors from our local MB dealer and buy Textar brake pads online. Perhaps the new parts you're using caused the fit problem.

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Fred Hoelzle