If you consider that the model was created to be constructed from wood, each individual component would be cut from appropriate material. It's more than likely your current approach will not finish well for that reason.

I've take others' plans for wood projects but used the flat files to duplicate on the 3D printer. The gears, for example, will print flat on the bed, providing reasonably good detail. Each component would have to be printed and checked for fit, as 3D printers tend to expand a dimension slightly and cause interference on tight designs. Your holes may be dimensioned for 3 mm, for example, but will print at 2.8 mm preventing that 3 mm pin from fitting, especially if it printed at 3.2 mm diameter. These numbers may be exaggerations to more easily present the concept.

What software did you use to convert the original plans to an STL file? I expect that it is powerful enough to allow you to create each component as described above.