it's suppose to be close, but not touch the clutch cover.
Did you also replace the bushing?
Do you have sideways play in the pedal?
If, Yes to the bushing, and No to the play, your mount "flap" (the eye welded to the frame) could be skewed, I had this happen to my EC in a hard crash that broke both mount and pedal, when replaced the pedal touched the clutch cover, I just bend the "flap" back in place and had no issues since then..