Cyclone 3 LVPECL

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I cannot find which dedicated clock pins go with a specific I/O bank

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??? The information can be found in many places, e.g. Quartus Pin Planner tool, Quartus pinout file, Cyclone III device specific pin tables.

Regarding your original question, it's true, that the Cyclone III hardware manual clearly states LVPECL only supported for dedicated clock inputs. I can't see a clear reason for this restriction however, you should have no problems to generate LVPECL compatible levels from a differential output with a resistor network, similar to LVDS_E_3R IO-standard, at least for a specified fanout.