Reading that, I would bet that something is going on with the mount or the mount driver.
Something odd, but my troubleshooting steps would be :
1. Run PHD2 and connect only the cam, not the mount. Do you still have time outs?
2. I would create a fresh SD card with Astroberry or with AstroPi3 script, and run try again with the mount connected. Do you still have time outs?
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