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Hi, that is a long thread (didn't read it), but regarding the 4mm retraction, I recall a similar discussion for cr10's, and folks (with microswiss hot ends) noted they were using >4mm with success, but nothing that seemed crazy. I use 5.2mm @ 45mm/s with my CR10 S Pro with a Micro Swiss, and have had zero issues (that I can recall). 4mm was too low for many of the filaments I have tried, so I had to go higher. The 4mm suggestion / warning was in a manufacturer produced setup video on yt for my hot end as well (CR10S Pro). Some people will also recommend an oiler to help with chronic clogging, but I have no experience with those - just mentioning it if things get out of hand and you have no better option. I'd suggest checking the hot end cooling fan just in case.

Excessive retractions in the end gcode have caused me problems in the past with my Ender3, it was evident in my case when there was a perfect print on the bed and the next one couldn't start due to the clog. My start gcode does a purge line so anything that oozes from the nozzle is not an issue anyway.

Something else that occurred to me since your printer had issues early in the print - it sounds like a problem I had when the nozzle was too low for the first layer. I had problems like what you described when the nozzle z offset was not high enough to allow the correct amount of filament to come out, or my bed was not level and one side of the first layer was fine and the other was almost non-existent. The nozzle was effectively capped off for part of most of the first layer which I think compounded the retractions in that layer causing the clogs.

What was the retraction value you were using prior, that was causing problems?