I've been using the 1865 Illinois State Census at FamilySearch. Between the poor handwriting, the faded ink, and the non-English names, it has been easier to search page by page to find the people I am looking for.
If you have people you cannot find in a specific record and you have a reasonably good idea of where they were living, go back and manually search the records if at all possible. I've found quite a few of my 1865 people in the Illinois State Census--most of them by searching one page at a time. Sometimes that's what has to happen.
And the guy in Chicago I may never find.
We've mentioned this before, but the need to sometimes manually search is one that most of us need to remember from time to time, myself included.