Lots of links here:
http://www.pawneecountyhistory.com/yesteryear/It looks like their contact info is "contact webmaster"; not too promising, but worth a try.
This doesn't look too helpful:
http://genealogytrails.com/neb/pawnee/I'm not sure about this one:
http://www.epodunk.com/cgi-bin/genealogyInfo.php?locIndex=22424I was looking for a transcription of the cemetery. Sometimes they show up somewhere besides findagrave. It might still be out there and I didn't find it.
As Sandra suggested, try the local library. They are usually helpful--the smaller the town the more helpful they are. And they probably have copies of the local newspaper for the time period on microfilm, if they are anywhere.
His death record, if it exists, is the most likely place for his parents' names. That is, if there is one, and if his survivors knew what his parents' names were.
I can't think of another record that would call for the names of his parents. Definitely not his son's war record, - that wouldn't even ask for the son's own parents' names, unless somehow there was a pension file and they were entitled to it.
edited to add:
Naturalization papers might provide an exact date and place of birth, which would go a long way toward confirming his parentage, unless there were too many Scotts in the area to narrow it down to one couple.
Any siblings? any in the US? Have you looked for their records?