What do you mean by a side column?
A typical ballot could have two columns of offices. For each office there are a number of candidates and ovals to mark one's choices. In the column the candiadates names appear on the left side and the voting ovals on the right. It is possible to leave some of the names for races off the ballot if it varies by precinct in the county. Those names can be printed on a generic ballot for the voter during check-in. The printing shouldn't interfere with the scanned ovals.
How would you ensure that I got the right combination of US representatives, state board of education, state senators and representatives, county commissioners, constables, and JPs on my ballot?
If the paper is alignhed correctly there shoudl be little problem. Tnhe addition of a printed bar code or equivalent can be used to detect misaligned ballots. In any case the ballots are paper and available for a recount.
In many cases, the district offices are for 4 years, with staggered terms, so I may or may not vote for a state senator, for example, based on my precinct. There are also provisions for removing uncontested races from the ballot.
I was only proposing to print the races that were on the current ballot. In IL uncontested races must remain on the ballot.
How would you check for undervotes or overvotes?
The bar code I suggested earlier can also notify the reader about the expected fields that should be marked.
How large of ballot paper is required for 100 races?
Cook county judicial ballots are a problem for any system of voting.