Using notepad++, there is a very efficient way to compare two eQUEST pd2 or *.inp files. This also works with EnergyPlus, and basically any two text based files. Check out the video and I'll show you how.
Notepad++ is a lightweight, must-have program for energy-modelers. I've fixed numerous complex eQUEST issues with the functionality. It's like wordpad, but on steroids (and yet somehow just as fast or faster)