My little fan holder also added 3-4 mm of space under the arduino. The bolts are barely threaded into the nuts and I need to replace them with longer ones.

I don't have conclusive proof, it just worked for me - went from 100% failure rate after 4 hours of printing - sample of 3 or four prints, to 100% success, sample of 2 prints. I would try this before any other fix. Note, not an issue when printing from SD, those ran fine all the way through. printing from SD is the best way to go for long prints especially if your pc is in any way unstable.

I originally looked at having the fan try to cover the arduino as well but the headers and connectors really box it in completely. for a permanent solution I would like to figure out a mount that can cover the stepper drivers and also direct some airflow between the arduno and the plywood frame.