What you have is a graph (in the computing sense) of steps that happen along two parallel lines, with a bunch of steps that may or may not stop others from happening on the other line.

I'd look at things like a VCS's history graph, or video game skill trees to see how this could be visualized.

I'd break it down into text files with:

    - One file that covers all procedures
    - One file per procedure (or sub procedure)
    - One structured paragraph per step
    - A per-step list of tool/supply dependencies

This would be manageable in most VCS's, and could easily be broken out for work by multiple people. You could also have tools that automatically generates a list of all the tools used in a step/procedure, and then checks it against other procedures to avoid needing two of a tool when only one is available.