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Just an Idea for FAN positioning: What do you think about repositioning the fan like placed here: https://www.thingiverse.com/thing:3690822 It should solve some issue, better airflow, vertical position (smaller change for filament to drop into the fan from the table). Maybe should pull out a little to back-way, to left some place for the 30A relay.

I'm not sure about temperature control for fan, because there is no chance to measure correctly each part of the box, or if you try that will be too much thermistor, connection, and cables again. Or maybe with octoprint collect all data from mainborad and RPI? The controll itself possible, write a module for it and controll a power mosfet with PWM, with a digispark attiny it's easy, cheap and small, working from 5V, can communicate with octoprint on any protocol like I2C or serial. I'm just wondering based on what kind of measures?

Ender 3 universal rear electronics case REMIX