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I have done something similar as well. Although, instead of starting from the pinout spreadsheet from Altera, I imported the fitter pin-out file into Excel.
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Excellent! You have Pads following the names you assigned in Quartus. I'm have Quartus following the signal names I assigned in Eagle. Same idea, different direction.
Using the Altera spreadsheet gave me all the power/gnd/and any unused signals, including NC and DNU pins. Not only did this keep my library editor happy, it also let me generate the entire footprint from the script.
I also figure that when I swapped pins in my schematic design to ease routing, this information will eventually make its way to Quartus.
So far, I can't quite get all the info into the pin assignment editor, but all the signal names are there. Hopefully, I'll figure out how to get direction and other information eventually. For now, I still do that manually.
Both of our ways still need some manual intervention, but it sure beats the full manual way of doing it.
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