You did not change thermal compound. Your CPU was running hours after hours at temps like 100c and your GPU did exactly the same, your Solder got ruined and thats whats must be happening...
When disassembling a console, that "kind of" thermal compound what used to make like 20% contact between cpu/gpu and cooler gets completely ruined and after that you enjoy 1% of thermal contact if not even less.
I got a CECH21xx my self here... Running at 59c/55c, before I changed thermal compound she was 77/70
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