Oh man, you just described my worst nightmare! I once had to deal with a 1995 Allen-Bradley PLC-5 that was running a critical bottling line. The original programmer had retired 15 years earlier, all documentation was lost in a flood, and there were zero backups. The plant manager just said 'make it work' when we needed to add a new sensor.
Here's how I cracked it: First, I spent days just watching the machine run, taking notes on what inputs triggered what outputs. I printed out the ladder logic (thankfully the PLC still worked!) and started mapping every rung with colored highlighters - green for inputs, red for outputs, yellow for timers. The real breakthrough came when I found an old maintenance logbook in a dusty cabinet that had handwritten notes about some of the I/O addresses.
I created a state transition diagram by manually tracing through the logic during different machine cycles. The key was identifying the main control routines versus safety interlocks. It took about three weeks of painstaking work, but eventually I could understand about 80% of the logic. The remaining 20% were those weird 'temporary fixes' the original programmer had patched in over the years - those I just had to test carefully and document for the next poor soul who'd have to deal with it!