LVPECL with VCC of 3.3V on a Cyclone3

The problem is, that Cyclone III doesn't provide a differential input standard for VCCIO of 1.8V. You are able to divide down a single ended PECL output to met the SSTL-18 reference voltage, but the signal swing is below the specification, and I fear, the level will be also affected by temperatur variations. Without a true differential input, it's difficult to achieve reliable operation.

Setting the comparators VCCO to minimal speicified 2.7V may bring you nearer to an acceptable solution. Personally, I would prefer external LVDS receivers.