Hello Kaed,
Assuming you have similar geological formations or lithological layers in all the boreholes but at different elevations, you might look at what groupings of lithology intervals you would want to create as hydrogeological layers in a groundwater model. This would set up the conceptual 3-D plan for your model. I am not familiar with Python software, but if you can import the data into an Excel worksheet you can look at defining the X, Y, and elevation points for top of each layer in the data and create a single file of X, Y, and elevation for each layer. It would take a bit of manual labor to create a separate worksheet for each layer (there may be ways to do this using more automated means but I am not knowledgeable on that). But once saved as CSV's, you can import these into ModelMuse (free user interface for MODFLOW) to create an accurate 3-D conceptual model and build your groundwater model from there, creating areas of hydraulic conductivity, boundary conditions, recharge, etc.
Best wishes for a successful outcome!
Geobob