This is, I think, the final design for the function casing for the Logical Engine. I took 1/2" acrylic sheet and fed it to the ShopBot, making a series of sections, each of which can be lifted entirely up and out of the casing if they need to be repaired. An additional guide screws on the outside which further aligns the rods.
This idea was sparked by a member of the DIY Book Scanner forum, Charles Morrill.
Closeup of the alignment system.
The horizontal slots were easy to make with the ShopBot, but those slots would allow the rods to shift horizontally. The outside guides simultaneously restrict their horizontal movement and precisely vertically position each horizontal segment to be one inch apart (plus or minus a few mils).
The rods still need to be significantly straight. I found that the steel has a simple bow to it that can be corrected by applying a force to bow the steel in the other direction. They don't appear to be randomly twisted or bent, so hopefully I wouldn't have to go the route of destressing with heat.